bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gram Type-Specific Broad-Range PCR Amplification for Rapid Detection of 62 Pathogenic Bacteria
Authors: Klausegger Alfred , Hell Markus , Berger Alexandra , Zinober Kerstin , Baier Sabine , Jones Neil , Sperl Wolfgang , Kofler Barbara 
Published: December 2019

ABSTRACT
Broad-range PCR has proven to be useful for the detection of bacteria. A set of broad-range PCR primers directed against conserved regions in the 16S rRNA gene was designed to specifically amplify either gram-positive or gram-negative bacteria. The gram type-specific broad-range PCR correctly classified all 62 pathogenic species tested.
Candida catenulata
Fungemia in a Cancer Patient
Authors: Radosavljevic Mirjana , Koenig Hélène , Letscher-Bru Valérie , Waller Jocelyn , Maloisel Fréderic , Lioure Bruno , Herbrecht Raoul 
Published: December 2019

ABSTRACT

We report the first case of fungemia due to
Candida catenulata
, a contaminant of dairy products.
C. catenulata
was isolated from three blood cultures of a patient with gastric cancer. The patient failed to respond to fluconazole but recovered after treatment was switched to amphotericin B. In vitro,
C. catenulata
was susceptible to amphotericin B and itraconazole and was also susceptible to fluconazole in dose-dependent manner. The likely portal of entry was the digestive tract, as the patient often ate cheese and had multiple gastric ulcerations.
Comparative Analysis and Serovar-Specific Identification of Multiple-Banded Antigen Genes of
Ureaplasma urealyticum
Biovar 1
Authors: Kong Fanrong , Zhu Xuejun , Wang Weizhen , Zhou Xiangzhao , Gordon Susanna , Gilbert Gwendolyn L. 
Published: December 2019

ABSTRACT

Ureaplasma urealyticum
is a causative agent of nongonococcal urethritis and is implicated in the pathogenesis of several other diseases. The species is divided into 14 serovars and two biovars, of which biovar 1 is most commonly isolated from clinical specimens. Reported associations between individual serovars and diseases have been difficult to confirm because of practical difficulties with serotyping. The multiple-banded antigen (MBA) is the predominant
U. urealyticum
antigen recognized during infections in humans and probably has a significant role in virulence. The 5′ end of the MBA gene is relatively conserved but contains biovar, and possibly serovar, specificity. The 5′ ends of the MBA genes of standard strains of
U. urealyticum
biovar 1, consisting of serovars 1, 3, 6, and 14, were amplified, cloned into pUC19, and sequenced to identify serovar-specific differences. The 5′ end of the MBA gene sequence of serovar 3 was identical with the previously published sequence and differed by only three bases from that of serovar 14. Significant differences between the MBA gene sequences allowed biovar 1 to be divided into two subgroups, containing serovars 3/14 and serovars 1 and 6, respectively, using primers UMS-125–UMA269 and UMS-125–UMA269′. Serovars 1 and 6 were distinguished by restriction enzyme analysis of the amplicon and/or by PCR specific for serovar 6. These methods were used to identify and type
U. urealyticum
in 185 (46.3%) of 400 genital specimens from women. Biovar 1 was detected in 89.2% and biovar 2 in 18.3% of positive specimens. Of 165 specimens containing
U. urealyticum
biovar 1, 22.2% contained more than one serovar and 46.7, 46.1, and 25.5% contained serovars 1, 3/14, and 6, respectively.
U. urealyticum
was found in a significantly higher proportion of pregnant women than in sex workers and other women attending a sexually transmissible diseases clinic (
P
< 0.01). The methods described are relatively rapid, practicable, and specific for serotyping isolates and for direct detection and identification of individual serovars in clinical specimens containing
U. urealyticum
biovar 1.
The
Borrelia burgdorferi
37-Kilodalton Immunoblot Band (P37) Used in Serodiagnosis of Early Lyme Disease Is the
flaA
Gene Product
Authors: Gilmore Robert D. , Murphree Rendi L. , James Angela M. , Sullivan Sarah A. , Johnson Barbara J. B. 
Published: December 2019

ABSTRACT

The 37-kDa protein (P37) of
Borrelia burgdorferi
is an antigen that elicits an early immunoglobulin M (IgM) antibody response in Lyme disease patients. The
P37
gene was cloned from a
B. burgdorferi
genomic library by screening with antibody from a Lyme disease patient who had developed a prominent humoral response to the P37 antigen. DNA sequence analysis of this clone revealed the identity of P37 to be FlaA, an outer sheath protein of the periplasmic flagella. Recombinant P37 expression was accomplished in
Escherichia coli
by using a gene construct with the leader peptide deleted and fused to a 38-kDa
E. coli
protein. The recombinant antigen was reactive in IgM immunoblots using serum samples from patients clinically diagnosed with early Lyme disease that had been scored positive for
B. burgdorferi
anti-P37 reactivity. Lyme disease patient samples serologically negative for the
B. burgdorferi
P37 protein did not react with the recombinant. Recombinant P37 may be a useful component of a set of defined antigens for the serodiagnosis of early Lyme disease. This protein can be utilized as a marker in diagnostic immunoblots, aiding in the standardization of the present generation of IgM serologic tests.
Measurement of Urinary Lactoferrin as a Marker of Urinary Tract Infection
Authors: Arao Shinsuke , Matsuura Shiro , Nonomura Mitsuo , Miki Kanji , Kabasawa Keigo , Nakanishi Hisao 
Published: December 2019

ABSTRACT
The usefulness of the measurement of urinary lactoferrin (LF) released from polymorphonuclear leukocytes and of an immunochromatography test strip devised for measuring urinary LF for the simple and rapid diagnosis of urinary tract infections (UTI) was evaluated. Urine specimens were collected from apparently healthy persons and patients diagnosed as suffering from UTI. In the preliminary study, the LF concentrations in 121 normal specimens and 88 specimens from patients (60 with UTI) were quantified by an enzyme-linked immunosorbent assay. The LF concentration was 3,300.0 ± 646.3 ng/ml (average ± standard error of the mean) in the specimens from UTI patients, whereas it was 30.4 ± 2.7 ng/ml and 60.3 ± 14.9 ng/ml in the specimens from healthy persons and the patients without UTI, respectively. Based on these results, a 200-ng/ml LF concentration was chosen as the cutoff value for negativity. Each urine specimen was reexamined with the newly devised immunochromatography (IC) test strip to calculate the indices of efficacy. Based on the cutoff value, it was calculated that the sensitivity, specificity, and positive and negative predictive values of the IC test were 93.3, 89.3, 86.2, and 94.9%, respectively, compared with the results of the microscopic examination of the urine specimens for the presence of leukocytes. The respective indices for UTI were calculated as 95.0, 92.9, 89.7, and 96.6%. The tests were completed within 10 min. These results indicated that urine LF measurement with the IC test strip provides a useful tool for the simple and rapid diagnosis of UTI.
Genetic Diversity and Population Structure of
Vibrio cholerae
Authors: Beltrán Pilar , Delgado Gabriela , Navarro Armando , Trujillo Francisca , Selander Robert K. , Cravioto Alejandro 
Published: December 2019

ABSTRACT

Multilocus enzyme electrophoresis (MLEE) of 397
Vibrio cholerae
isolates, including 143 serogroup reference strains and 244 strains from Mexico and Guatemala, identified 279 electrophoretic types (ETs) distributed in two major divisions (I and II). Linkage disequilibrium was demonstrated in both divisions and in subdivision Ic of division I but not in subdivision Ia, which includes 76% of the ETs. Despite this evidence of relatively frequent recombination, clonal lineages may persist for periods of time measured in at least decades. In addition to the pandemic clones of serogroups O1 and O139, which form a tight cluster of four ETs in subdivision Ia, MLEE analysis identified numerous apparent clonal lineages of non-O1 strains with intercontinental distributions. A clone of serogroup O37 that demonstrated epidemic potential in the 1960s is closely related to the pandemic O1/O139 clones, but the nontoxigenic O1 Inaba El Tor reference strain is not. A strain of serogroup O22, which has been identified as the most likely donor of exogenous
rfb
region DNA to the O1 progenitor of the O139 clone, is distantly related to the O1/O139 clones. The close evolutionary relationships of the O1, O139, and O37 epidemic clones indicates that new cholera clones are likely to arise by the modification of a lineage that is already epidemic or is closely related to such a clone.
Body Lice as Tools for Diagnosis and Surveillance of Reemerging Diseases
Authors: Roux Veronique , Raoult Didier 
Published: December 2019

ABSTRACT

Body lice are vectors of three bacteria which cause human disease:
Rickettsia prowazekii
, the agent of epidemic typhus;
Bartonella quintana
, the agent of trench fever; and
Borrelia recurrentis
, the agent of relapsing fever. A recrudescence of body lice is being observed as the numbers of individuals living under social conditions which predispose individuals to infestation have increased. Because this phenomenon may lead to the reemergence of infections transmitted by body lice, we aimed to assess the occurrence and prevalence of the three agents described above in more than 600 body lice collected from infested individuals in the African countries of Congo, Zimbabwe, and Burundi, in France, in Russia, and in Peru. The presence of the three bacteria in each louse was determined by specific PCR amplification, and the identities of the organisms detected were confirmed by determination of the nucleotide base sequences of the amplification products. Using this approach, we were able to confirm the presence of
R. prowazekii
in lice collected from refugees in Burundi, among whom typhus was epidemic, and the presence of
B. quintana
in lice collected from all locations except the Congo.
B. recurrentis
was never found. Molecular approaches are convenient tools for the detection and identification of bacterial DNA in body lice and for the epidemiological study of louse-borne bacteria from countries where no medical and biological laboratory facilities are available.
Usefulness of PCR and Antigen Latex Agglutination Test with Samples Obtained by Transthoracic Needle Aspiration for Diagnosis of Pneumococcal Pneumonia
Authors: García Amparo , Rosón Beatriz , Pérez José Luis , Verdaguer Ricard , Dorca Jordi , Carratalà Jordi , Casanova Aurora , Manresa Frederic , Gudiol Francesc 
Published: December 2019

ABSTRACT

In a large number of cases, the etiology of community-acquired pneumonia (CAP) is not established. Some cases are probably caused by
Streptococcus pneumoniae
. Transthoracic needle aspiration (TNA) culture has a limited sensitivity which might be improved by antigen detection or gene amplification techniques. We evaluated the capacity of a PCR assay and a latex agglutination test to detect
S. pneumoniae
in samples obtained by TNA from 95 patients with moderate-to-severe CAP. Latex agglutination and PCR had sensitivities of 52.2 and 91.3%, specificities of 88.7 and 83.3%, positive predictive values of 62.3 and 65.6%, and negative predictive values of 83.3 and 96.5%, respectively, when culture techniques were used as the “gold standard.” When we considered expanded criteria for the diagnosis of pneumococcal pneumonia as a standard for our calculations, latex agglutination and PCR had sensitivities of 53.6 and 89.7%, specificities of 93.0 and 90.0%, positive predictive values of 78.9 and 81.3%, and negative predictive values of 80.3 and 94.7%, respectively. The additional diagnosis provided by the PCR assay compared to latex agglutination was 12.2% (95% confidence interval of the difference from 0.4 to 20.1%). PCR was more sensitive than TNA culture, particularly in patients who had received prior antibiotic therapy (83.3 versus 33.3%). Although PCR is a very sensitive and specific technique, it has not proved to be cost-effective in clinical practice. Conversely, latex agglutination is a fast and simple method whose results might have significant implications for initial antibiotic therapy.
Dual Qualitative-Quantitative Nested PCR for Detection of JC Virus in Cerebrospinal Fluid: High Potential for Evaluation and Monitoring of Progressive Multifocal Leukoencephalopathy in AIDS Patients Receiving Highly Active Antiretroviral Therapy
Authors: García de Viedma Darío , Alonso Roberto , Miralles Pilar , Berenguer Juan , Rodriguez-Créixems Marta , Bouza Emilio 
Published: December 2019

ABSTRACTJC polyomavirus (JCV) is the causative agent of progressive multifocal leukoencephalopathy (PML), a central nervous system infection that mainly affects AIDS patients. The extensive application of highly active antiretroviral therapy (HAART) is leading to the appearance of “long-term” survival PML patients. A reliable and feasible qualitative-quantitative test for both the detection of JCV and follow-up of its viral burden in this emerging group of patients is clearly required. With this aim, a dual qualitative-quantitative nested PCR is presented in this study for the analysis of JCV DNA in cerebrospinal fluid (CSF). Two newly designed internal controls, one competitive and the other noncompetitive, have been constructed to adapt this PCR to either measure the JCV burden or to allow a highly confident determination of JCV presence or clearance. The analytical sensitivity of the technique allows the detection of 0.01 fg (three genomes) of JCV DNA. Its qualitative application has been evaluated by analyzing single CSF samples from a group of 17 patients with PML and a control group of 20 patients with diverse neurological conditions other than PML, yielding sensitivity and specificity values of 100 and 90%, respectively. The quantitative application has been evaluated in vitro in blind tests with samples including serial dilutions of JCV, and in all cases the samples were successfully ordered considering the JCV titer. The dual quantitative-qualitative application offered by this nested PCR may provide an answer to the new requirements for evaluating and finely monitoring PML in AIDS patients receiving HAART.
Spread of Amikacin Resistance in
Acinetobacter baumannii
Strains Isolated in Spain Due to an Epidemic Strain
Authors: Vila Jordi , Ruiz Joaquim , Navia Margarita , Becerril Berta , Garcia Isabel , Perea Sofia , Lopez-Hernandez Inmaculada , Alamo Isabel , Ballester Frederic , Planes Anna M. , Martinez-Beltran Jesus , De Anta Teresa Jimenez 
Published: December 2019

ABSTRACT

Sixteen amikacin-resistant clinical
Acinetobacter baumannii
isolates from nine different hospitals in Spain were investigated to determine whether the high incidence of amikacin-resistant
A. baumannii
was due to the dissemination of an amikacin-resistant strain or to the spread of an amikacin resistance gene. The epidemiological relationship studied by repetitive extragenic palindromic PCR and low-frequency restriction analysis of chromosomal DNA showed that the same clone was isolated in eight of nine hospitals, although other clones were also found. The strains were studied for the presence of the
aph(3′)-VIa
and
aac(6′)-I
genes, which encode enzymes which inactivate amikacin, by PCR. All 16 clinical isolates had positive PCRs with primers specific for the amplification of the
aph(3′)-VIa
gene, whereas none had a positive reaction for the amplification of the
aac(6′)-I
gene. Therefore, the high incidence of amikacin resistance among clinical
A. baumannii
isolates in Spain was mainly due to an epidemic strain, although the spread of the
aph(3′)-VI
gene cannot be ruled out.
Assessment of Use of the COBAS AMPLICOR System with BACTEC 12B Cultures for Rapid Detection of Frequently Identified Mycobacteria
Authors: Ninet B. , Rohner P. , Metral C. , Auckenthaler R. 
Published: December 2019

ABSTRACT

The use of the COBAS AMPLICOR System (Roche Molecular Diagnostics, Basel, Switzerland), the only automated system for PCR testing, was evaluated for a rapid identification of mycobacteria with positive BACTEC 12B cultures. Two hundred ninety-six specimens with a growth index of ≥30 were analyzed for the presence of
Mycobacterium tuberculosis
complex,
Mycobacterium avium
, and
Mycobacterium intracellulare
. Compared to traditional methods and provided that samples with PCR inhibition are retested at a 1:10 dilution, the sensitivity and specificity of the COBAS AMPLICOR System with BACTEC 12B cultures were 100 and 98%, respectively. The COBAS AMPLICOR method is rapid and reliable for identifying the most common mycobacteria in cultures.
Human Phaeohyphomycotic Osteomyelitis Caused by the Coelomycete
Phomopsis
Saccardo 1905: Criteria for Identification, Case History, and Therapy
Authors: Sutton Deanna A. , Timm William D. , Morgan-Jones Gareth , Rinaldi Michael G. 
Published: December 2019

ABSTRACT

The Sphaeropsidales, coelomycetous fungi producing asexual conidia within enclosed conidiomata (pycnidia), are saprobic on numerous vascular plants. Despite their ubiquitous nature, only a limited number of genera have been documented as causing human disease. We report what we believe to be the first human case of osteomyelitis due to a
Phomopsis
species in a chronically immunosuppressed female. The patient developed a subcutaneous abscess on the distal phalanx of the right fourth finger complicated by osteomyelitis. Operative specimens revealed fungal hyphae and a pure culture of mould. The patient was treated with a 6-month course of itraconazole. At 16 months of follow-up, she remained free of recurrence.
Phomopsis
species differ from the similar, more frequently reported
Phoma
species by having immersed, thick-walled, multiloculate conidiomata and by the production of alpha (short, ellipsoidal) and beta (long, filamentous) conidia.
Comparison of Simple and Rapid Methods for Identifying Enterococci Intrinsically Resistant to Vancomycin
Authors: Hanson Kevan L. , Cartwright Charles P. 
Published: December 2019

ABSTRACT

Three different methodologies, reduction of litmus milk (LM) and acidification of arabinose (ARA), acidification of methyl-α-
d
-glucopyranoside (MGP), and rapid motility (RM), for differentiating isolates of
Enterococcus casseliflavus
and
Enterococcus gallinarum
(intrinsically vancomycin-resistant enterococci [IVRE]) from
Enterococcus faecalis
and
Enterococcus faecium
were evaluated. All 33 isolates of
E. faecalis
tested reduced LM within 4 h and were negative in all other tests, while the 53 isolates of
E. faecium
were ARA positive only. In contrast, 45 of 46 (98%) IVRE isolates examined (26
E. casseliflavus
and 20
E. gallinarum
isolates) acidified MGP, 41 of 46 (89%) were LM and ARA positive, and 45 of 46 (98%) were RM positive. Acidification of MGP was therefore the single most useful test for differentiating IVRE from vancomycin-resistant
E. faecium
and
E. faecalis
; however, a combination of LM-ARA and RM testing enabled the correct designation of organisms without the need for overnight incubation.
Comparison of the API Candida System with the AUXACOLOR System for Identification of Common Yeast Pathogens
Authors: Campbell Colin K. , Davey Kate G. , Holmes Ann D. , Szekely Adrien , Warnock David W. 
Published: December 2019

ABSTRACT
Two commercial systems for the identification of yeasts were evaluated by using 159 clinical isolates that had also been identified by conventional biochemical and morphological methods. The API Candida system correctly identified 146 isolates (91.8%), and the AUXACOLOR system correctly identified 145 isolates (91.2%). However, of the 146 isolates identified by the API Candida system, 23 required supplemental biochemical tests or morphological assessment to obtain the correct identification. The AUXACOLOR system gave no identification in 13 cases (8.2%), while the API Candida system gave an unreadable profile in only one case. Incorrect identifications were more common with the API Candida system (12 isolates; 7.5%) than with the AUXACOLOR system (1 isolate; 0.6%).
Chronic Urinary Tract Infection Due to
Candida utilis
Authors: Hazen Kevin C. , Theisz Gordon W. , Howell Susan A. 
Published: December 2019

ABSTRACT

An elderly male was seen at an outpatient urology clinic over a period of 3 years with repeat urine specimens containing 10
4
to 10
5
CFU of a “
Candida
species, not
C. albicans
.” The urine specimens were described as infected due to the presence of pyuria, but no antifungal therapy was administered. On two occasions, the patient presented to the emergency room and urine specimens were sent to the clinical microbiology laboratory. On both occasions, a yeast was isolated at concentrations of >10
5
CFU/ml. The organism was identified as the anamorphic yeast
Candida utilis
(teleomorph:
Pichia jadinii
) by conventional methods. Molecular methods, including karyotyping and restriction enzyme analysis, confirmed that the isolates were identical and were
C. utilis
. The patient developed benign prostatic hypertrophy and chronic obstructive pulmonary disease during the 3-year course. This report is the first demonstration of the isolation of the industrially important yeast
C. utilis
from a urinary tract infection. In the present case, the organism was associated with chronic, symptomatic disease. The significance of this unusual, low-virulence isolate from a case of urinary tract infection is discussed.
Cryptococcus neoformans
var.
grubii
: Separate Varietal Status for
Cryptococcus neoformans
Serotype A Isolates
Authors: Franzot Sarah P. , Salkin Ira F. , Casadevall Arturo 
Published: December 2019

ABSTRACT

Cryptococcus neoformans
var.
neoformans
presently includes isolates which have been determined by the immunologic reactivity of their capsular polysaccharides to be serotype A and those which have been determined to be serotype D. However, recent analyses of the
URA5
sequences and DNA fingerprinting patterns suggest significant genetic differences between the two serotypes. Therefore, we propose to recognize these genotypic distinctions, as well as previously reported phenotypic differences, by restricting
C. neoformans
var.
neoformans
to isolates which are serotype D and describing a new variety,
C. neoformans
var.
grubii
, for serotype A isolates.
Aerobic and Anaerobic Microbiology of Surgical-Site Infection Following Spinal Fusion
Authors: Brook Itzhak , Frazier Edith H. 
Published: December 2019

ABSTRACT

The aerobic and anaerobic microbiology of surgical-site infections (SSI) following spinal fusion was retrospectively studied. This was done by reviewing the clinical and microbiological records at the Naval Hospital in Bethesda, Md., from 1980 to 1992. Aspirates of pus from 25 infection sites showed bacterial growth. Aerobic bacteria only were recovered from 9 (36%) specimens, anaerobic bacteria only were recovered from 4 (16%), and mixed aerobic and anaerobic bacteria were recovered from 12 (48%). Sixty isolates were recovered: 38 aerobes (1.5 isolates per specimen) and 22 anaerobes (0.9 isolate per specimen). The predominant aerobes were
Escherichia coli
(
n
= 8) and
Proteus
sp. (
n
= 7). The predominant anaerobes were
Bacteroides fragilis
group (
n
= 9) and
Peptostreptococcus
sp. (
n
= 6) isolates. An increase in recovery of
E. coli
and
B. fragilis
was noted in patients with bowel or bladder incontinence. This study highlights the polymicrobial nature of SSI and the importance of anaerobic bacteria in SSI following spinal fusion.
Use of Restriction Fragment Analysis and Sequencing of a Serotype-Specific Region To Type Adenovirus Isolates
Authors: Li Quan-Gen , Henningsson Anna , Juto Per , Elgh Fredrik , Wadell Göran 
Published: December 2019

ABSTRACT
Restriction fragment analysis and sequencing of a serotype-specific region were used to type 12 and 2 clinical isolates, respectively. Both molecular methods produced clear-cut results that completely correlated with that of the neutralization test.