bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiological Analysis of
Salmonella enteritidis
Isolates from Humans and Broiler Chickens in Thailand by Phage Typing and Pulsed-Field Gel Electrophoresis
Authors: Boonmar Sumalee , Bangtrakulnonth Aroon , Pornrunangwong Srirat , Terajima Jun , Watanabe Haruo , Kaneko Ken-Ichi , Ogawa Masuo 
Published: December 2019

ABSTRACT

To determine the phage types (PT) of
Salmonella enteritidis
found in Thailand and to clarify the potential for human infection by
S. enteritidis
in broiler chicken meat, human and poultry isolates taken from Thailand between 1990 and 1997 were phage typed and analyzed by pulsed-field gel electrophoresis (PFGE). Ten different PT were found among the 302 isolates phage typed, with PT 4 being the most frequent in human (73.9%) and poultry (76.2%) isolates, followed by PT 1 (8.0%), 8 (3.6%), and 7a (2.2%) in human isolates and by PT 7a (4.9%), 1 (3.7%), and 12 (2.4%) in poultry isolates. Of the 53 isolates analyzed by PFGE, 45 showed an indistinguishable pattern (pattern A) by
Bln
I-digested PFGE and the other 8 isolates showed a very similar pattern that differed by only a few bands. These results indicate the spread of a genetically identical clone of
S. enteritidis
in humans and poultry in Thailand.
Gemella bergeriae
sp. nov., Isolated from Human Clinical Specimens
Authors: Collins Matthew D. , Hutson Roger A. , Falsen Enevold , Sjöden Berit , Facklam Richard R. 
Published: December 2019

ABSTRACT

Six strains of a hitherto-undescribed gram-positive, catalase-negative, facultatively anaerobic coccus from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains are genealogically homogeneous and constitute a new subline within the genus
Gemella
. The unknown bacterium was readily distinguished from
Gemella haemolysans
, the type species of the genus
Gemella
, and from
Gemella morbillorum
by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from clinical specimens be classified as
Gemella bergeriae
sp. nov. The type strain of
G. bergeriae
is CCUG 37817 (= strain 617-93).
Diagnostic Value of Monitoring Human Cytomegalovirus Late pp67 mRNA Expression in Renal-Allograft Recipients by Nucleic Acid Sequence-Based Amplification
Authors: Blok Marinus J. , Goossens Valere J. , Vanherle Sabina J. V. , Top Bert , Tacken Nicole , Middeldorp Jaap M. , Christiaans Maarten H. L. , van Hooff Johannes P. , Bruggeman Cathrien A. 
Published: December 2019

ABSTRACT
The diagnostic value of monitoring human cytomegalovirus (HCMV) late pp67 mRNA expression by nucleic acid sequence-based amplification (NASBA) after renal-allograft transplantation was evaluated. RNAs were isolated from 489 whole-blood specimens of 42 patients for the specific amplification of the late pp67 (UL65) mRNA. NASBA results were compared to results from the pp65 antigenemia assay, virus isolation by cell culture, and serology. The sensitivity value for NASBA proved to be higher than that for the antigenemia assay (50 versus 35%) for the detection of HCMV infection, while the sensitivity values of cell culture and NASBA were comparable (54 and 50%, respectively). NASBA detected the onset of HCMV infection simultaneously with cell culture and the antigenemia assay. Both the antigenemia assay and NASBA are very specific (100%) and highly predictive (100%) for the onset of HCMV infection. Antiviral therapy with ganciclovir resulted in negative results for cell culture, the antigenemia assay, and NASBA. In conclusion, monitoring HCMV pp67 mRNA expression by NASBA is a highly specific method for the detection of HCMV infection in renal-allograft recipients and is more sensitive than the antigenemia assay. Furthermore, NASBA can be used to monitor the progression of HCMV infections and the effect of antiviral therapy on viral activity.
Nosocomial Outbreak of
Klebsiella pneumoniae
Producing SHV-5 Extended-Spectrum β-Lactamase, Originating from a Contaminated Ultrasonography Coupling Gel
Authors: Gaillot Olivier , Maruéjouls Christophe , Abachin Éric , Lecuru Fabrice , Arlet Guillaume , Simonet Michel , Berche Patrick 
Published: December 2019

ABSTRACT

Klebsiella pneumoniae
resistant to ceftazidime was isolated from six adult women and two neonates hospitalized between July and November 1993 in the Department of Obstetrics and Gynecology of Boucicaut Hospital (Paris, France). The epidemiological investigation revealed a notably short delay (less than 48 h) between admission and contamination of the six adults and peripartum transmission to the neonates. The only environmental source of ceftazidime-resistant
K. pneumoniae
was the ultrasonography coupling gel used in the emergency room. Phenotypic (biotyping and antibiotyping) and genotypic (plasmid profile and pulsed-field gel electrophoresis) analysis of all the clinical isolates indicated the spread of a single strain. It produced SHV-5 and TEM-1 β-lactamases, as demonstrated by isoelectric focusing and gene sequencing. The risk of cross-contamination in ultrasonography procedures is usually low and had not been associated so far with bacteria producing an extended-spectrum β-lactamase (ESBL). Furthermore, this is the first time an epidemic of an SHV-5 ESBL-producing member of the family
Enterobacteriaceae
has been reported from a French hospital.
Identification of
Corynebacterium amycolatum
and Other Nonlipophilic Fermentative Corynebacteria of Human Origin
Authors: Wauters Georges , Van Bosterhaut Bernard , Janssens Michèle , Verhaegen Jan 
Published: December 2019

ABSTRACT

Four identification tests, proposed in addition to conventional methods, were evaluated with 320 fermentative nonlipophilic
Corynebacterium
strains: growth at 20°C, glucose fermentation at 42°C, alkalinization of sodium formate, and acid production from ethylene glycol. These tests were highly discriminant.
Corynebacterium amycolatum
displayed a unique profile, allowing it to be distinguished from similar species, such as
C. xerosis
,
C. striatum
, and
C. minutissimum.
Evaluation of PCR in Detection of
Mycobacterium tuberculosis
from Formalin-Fixed, Paraffin-Embedded Tissues: Comparison of Four Amplification Assays
Authors: Marchetti Giulia , Gori Andrea , Catozzi Lidia , Vago Luca , Nebuloni Manuela , Rossi M. Cristina , Esposti Anna Degli , Bandera Alessandra , Franzetti Fabio 
Published: December 2019

ABSTRACT

We compared the sensitivities and specificities of four nested PCR assays for the detection of
Mycobacterium tuberculosis
from formalin-fixed, paraffin-embedded tissues. Thirty-seven autopsy samples from human immunodeficiency virus-positive patients were analyzed: 15 were
M. tuberculosis
positive, 11 served as negative controls, and 11 were Ziehl-Neelsen positive without cultural confirmation of
M. tuberculosis
. Three genomic sequences (
mtp40
, 65-kDa antigen gene, and IS
6110
) with different molecular masses and numbers of repetitions within the
M. tuberculosis
genome were targeted. On the IS
6110
sequence, two fragments of different sizes (106 and 123 bp, respectively) were amplified with two separate pairs of primers. The highest sensitivity rates were obtained by amplifying the highly repetitive IS
6110
insertion sequence, and the different primers tested showed a sensitivity ranging from 80 to 87%. Amplification of the large 223-bp fragment of the
mtp40
sequence present in a single copy in the
M. tuberculosis
genome yielded a high rate of false-negative results, ranging from 66 to 80%. A poor sensitivity (from 47 to 60%) was also shown by PCR amplification of the 142-bp 65-kDa antigen gene. All the PCRs except that for the 65-kDa antigen gene showed a specificity of 100%. Moreover, different results were obtained with different dilutions of DNA, and DNA concentrations of 1 and 3 μg yielded the highest sensitivities depending upon which protocol was used. Application of the PCRs to the Ziehl-Neelsen-positive, culture-negative samples confirmed the sensitivities of the PCRs obtained with the control samples. In conclusion, PCR can successfully be used to detect
M. tuberculosis
from paraffin-embedded tissues and can be particularly useful in the validation of a diagnosis of tuberculosis in clinical settings in which the diagnosis is uncertain. However, the efficacy of PCR strictly depends on several amplification parameters such as DNA concentration, target DNA size, and the repetitiveness of the amplified sequence.
Detection of Human Immunodeficiency Virus Type 1 (HIV-1) RNA in Pools of Sera Negative for Antibodies to HIV-1 and HIV-2
Authors: Morandi Pierre-Alain , Schockmel Gérard A. , Yerly Sabine , Burgisser Philippe , Erb Peter , Matter Lukas , Sitavanc Radan , Perrin Luc 
Published: December 2019

ABSTRACT

A total of 234 pools were prepared from 10,692 consecutive serum samples negative for antibodies to human immunodeficiency virus type 1 (HIV-1) and HIV-2 collected at five virological laboratories (average pool size, 45 serum samples). Pools were screened for the presence of HIV-1 RNA by a modified commercial assay (Amplicor HIV-1 Monitor test) which included an additional polyethylene glycol (PEG) precipitation step prior to purification of viral RNA (PEG Amplicor assay). The sensitivity of this assay for HIV-1 RNA detection in individual serum samples within pools matches that of standard commercial assays for individual serum samples, i.e., 500 HIV-1 RNA copies per ml. Five pools were identified as positive, and each one contained one antibody-negative, HIV-1 RNA-positive serum sample, corresponding to an average of 1 infected sample per 2,138 serum samples. Retrospective analysis revealed that the five HIV-1 RNA-positive specimens originated from individuals who had symptomatic primary HIV-1 infection at the time of sample collection and who were also positive for p24 antigenemia. We next assessed the possibility of performing the prepurification step by high-speed centrifugation (50,000 ×
g
for 80 min) of 1.5-ml pools containing 25 μl of 60 individual serum samples, of which only 1 contained HIV-1 RNA (centrifugation Amplicor assay). The sensitivity of this assay also matches the sensitivities of standard commercial assays for HIV-1 RNA detection in individual serum samples. The results demonstrate that both assays with pooled sera can be applied to the screening of large numbers of serum samples in a time- and cost-efficient manner.
Characteristics of
Arthrobacter cumminsii
, the Most Frequently Encountered
Arthrobacter
Species in Human Clinical Specimens
Authors: Funke Guido , Pagano-Niederer Maja , Sjödén Berit , Falsen Enevold 
Published: December 2019

ABSTRACT

During a 2-year period, 10 strains of
Arthrobacter cumminsii
were isolated in or received by a Swiss routine clinical bacteriology laboratory, and 5 further isolates were referred to a Swedish bacteriology reference center over a 5-year period, making
A. cumminsii
the most frequently encountered
Arthrobacter
species in these two laboratories. The present report outlines the clinical features of the 15
A. cumminsii
strains and presents an extended biochemical characterization of this microorganism.
A. cumminsii
exhibits a unique cellular fatty acid pattern with the consistent presence of C

14:0
i

and C
14:0
fatty acids as well as relatively large amounts of C

16:0
i

and C
16:0
fatty acids usually not seen in other
Arthrobacter
spp. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was found to be a useful tool for confirmation of the identification of
A. cumminsii
. The MICs of 39 antimicrobial agents were determined, and it was demonstrated that aminoglycosides and quinolones had only weak activities against
A. cumminsii
strains, in contrast to their activities against most other coryneform bacteria. As a result of the extended characterization of
A. cumminsii
, an emended description of this species is presented. Due to the lack of
A. cumminsii
in established identification systems, it is most likely that this species is underdiagnosed in many routine clinical bacteriology laboratories.
Variables Affecting Results of Sodium Chloride Tolerance Test for Identification of Rapidly Growing Mycobacteria
Authors: Conville Patricia S. , Witebsky Frank G. 
Published: December 2019

ABSTRACT

The sodium chloride tolerance test is often used in the identification of rapidly growing mycobacteria, particularly for distinguishing between
Mycobacterium abscessus
and
Mycobacterium chelonae
. This test, however, is frequently unreliable for the identification of some species. In this study we examined the following variables: medium manufacturer, inoculum concentration, and atmosphere and temperature of incubation. Results show that reliability is improved if the test and control slants are inoculated with an organism suspension spectrophotometrically equal to a 1 McFarland standard. Slants should be incubated at 35°C in ambient air and checked weekly for 4 weeks. Growth on control slants should be critically evaluated to determine the adequacy of the inoculum; colonies should number greater than 50. Salt-containing media should be examined carefully to detect pinpoint or tiny colonies, and colonies should number greater than 50 for a positive reaction. Concurrent use of a citrate slant may be helpful for distinguishing between
M. abscessus
and
M. chelonae
. Molecular methodologies are probably the most reliable means for the identification of rapidly growing mycobacteria and should be used, if possible, when unequivocal species identification is of particular importance.
Sequence-Based Classification Scheme for the Genus
Legionella
Targeting the
mip
Gene
Authors: Ratcliff Rodney M. , Lanser Janice A. , Manning Paul A. , Heuzenroeder Michael W. 
Published: December 2019

ABSTRACT

The identification and speciation of strains of
Legionella
is often difficult, and even the more successful chromatographic classification techniques have struggled to discriminate newly described species. A sequence-based genotypic classification scheme is reported, targeting approximately 700 nucleotide bases of the
mip
gene and utilizing gene amplification and direct amplicon sequencing. With the exception of
Legionella geestiana
, for which an amplicon was not produced, the scheme clearly and unambiguously discriminated among the remaining 39
Legionella
species and correctly grouped 26 additional serogroup and reference strains within those species. Additionally, the genotypic classification of approximately 150 wild strains from several continents was consistent with their phenotypic classification, with the exception of a few strains where serological cross-reactivity was complex, potentially confusing the latter classification. Strains thought to represent currently uncharacterized species were also found to be genotypically unique. The scheme is technically simple for a laboratory with even basic molecular capabilities and equipment, if access to a sequencing laboratory is available.
Differentiation and Characterization of Enteroviruses by Computer-Assisted Viral Protein Fingerprinting
Authors: Holland Diane T. , Senne Jill , Peter C. R. , Urmeneta Connie , Connor J. D. 
Published: December 2019

ABSTRACTWe have developed and standardized a computerized method for the typing and characterization of enteroviruses with radiolabeled viral protein fingerprints. Enteroviral proteins were radiolabeled with [35S]methionine during growth in cell culture and were then separated by polyacrylamide gel electrophoresis. The dried gel was scanned, and from the resulting computer image (which resembled an autoradiogram) protein patterns were computer extracted and stored in a database. The enterovirus database contained community and prototype strains belonging to 20 different enteroviral serotypes. Each serotype has a discrete protein pattern, and the most important pattern differences for determining each type are in the region of the viral capsid proteins VP1, VP2, and VP3. When the database was challenged with 148 clinical enterovirus strains, 144 (97%) were correctly identified by using the correlation coefficient as a quantitative measure of relatedness between two patterns. This method can identify a type in a single test and represents a practical alternative to virus neutralization because it is less expensive, is much faster (3 rather than 10 days), and does not rely on any virus-specific reagents. The results also show that most of the strains currently isolated from the community have protein patterns different from those of their older prototype strains. Viral protein fingerprinting is an evolving, dynamic system for the typing and characterization of enteroviruses. The method is appropriate for use in clinical virology and reference laboratories for the typing of enteroviruses, for the study of the epidemiology of enteroviruses, and for surveillance of enteroviruses.
Virulence Properties of Shiga Toxin-Producing
Escherichia coli
(STEC) Strains of Serogroup O118, a Major Group of STEC Pathogens in Calves
Authors: Wieler L. H. , Schwanitz Anja , Vieler Elke , Busse Barbara , Steinrück H. , Kaper J. B. , Baljer G. 
Published: December 2019

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) strains of serogroup O118 are the most prevalent group among STEC strains in diarrheic calves in Germany (L. H. Wieler, Ph.D. thesis, University of Giessen, 1997). To define their virulence properties, 42 O118 (O118:H16 [
n
= 38] and O118:H− [
n
= 4]) strains were characterized. The strains displayed three different Stx combinations (Stx1 [36 of 42], Stx1 and Stx2 [2 of 42], and Stx2 [4 of 42]). A total of 41 strains (97.6%) harbored a large virulence-associated plasmid containing
hly
EHEC
(
hly
from enterohemorrhagic
E. coli
). The strains’ adhesive properties varied in relation to the eukaryotic cells tested. Only 28 of 42 strains (66.7%) showed localized adhesion (LA) in the human HEp-2 cell line. In contrast, in bovine fetal calf lung (FCL) cells, the number of LA-positive strains was much higher (37 of 42 [88.1%]). The locus of enterocyte effacement (LEE) was detected in 41 strains (97.6%). However, not all LEE-positive strains reacted positively in the fluorescence actin-staining (FAS) test, which indicated the attaching and effacing (AE) lesion. In HEp-2 cells, only 22 strains (52.4%) were FAS positive, while in FCL cells, the number of FAS-positive strains was significantly higher (38 of 42 [90.5%;
P
< 0.001]). In conclusion, the vast majority of the O118 STEC strains from calves (41 of 42 [97.6%]) have a high virulence potential (
stx
,
hly
EHEC
, and LEE). This virulence potential and the high prevalence of STEC O118 strains in calves suggest that these strains could be a major health threat for humans in the future. In addition, the poor association between results of the geno- and phenotypical tests to screen for the AE ability of STEC strains calls the diagnostic value of the FAS test into question.
Diverse and Related 16S rRNA-Encoding DNA Sequences in Prostate Tissues of Men with Chronic Prostatitis
Authors: Riley Donald E. , Berger Richard E. , Miner David C. , Krieger John N. 
Published: December 2019

ABSTRACT

Treatment of chronic prostatitis/chronic pelvic pain syndrome is often empirical because clinical culture methods fail to detect prostate-associated pathogens in >90% of patients. Previously, we tested a variety of specific-microorganism PCRs and began a DNA sequence study after we found that 77% of prostatitis patients were PCR positive for prokaryotic rRNA-encoding DNA sequences (rDNAs) despite negative cultures using optimal techniques. In the present study, 36 rDNA clones from 23 rDNA-positive patients were sequenced. This study represents more than twice the total rDNA sequence and more than twice the number of patients in the previous study. The increased number of patients and clones sequenced allowed enhanced phylogenetic analyses and refinements in our view of rDNA species inhabiting the prostate. A continuum of related rDNAs that might be arbitrarily described as two major groups of rDNAs and several minor groups was found. Sequences termed Pros A, identified in 8 (35%) of 23 rDNA-positive patients, grouped with
Aeromonas
spp. in phylogenetic studies. Sequences termed Pros B, identified in 17 (74%) of 23 rDNA-positive patients, were distinct from previously reported sequences, although all were >90% similar to known gram-negative bacteria. Of the nine patients for whom multiple rDNAs were sequenced, six had biopsy specimens containing rDNAs from more than one species. Four (17%) patients had rDNAs different from those of the Pros A and Pros B groups. Of these four, one patient had rDNA similar to that of
Flavobacterium
spp., another had rDNA similar to that of
Pseudomonas testosteroni
, and two patients had rDNAs <70% similar to known rDNAs. These findings suggest that the prostate can harbor bacteria undetectable by traditional approaches. Most of these diverse sequences are not reported in environments outside the prostate. The sequence similarities suggest adaptation of limited groups of bacteria to the microenvironment of the prostate. Further studies may elucidate the relationship of prostate-associated bacteria to chronic prostatitis/chronic pelvic pain syndrome.
Evaluation of North American Antibody Detection Tests for Diagnosis of Brucellosis in Goats
Authors: Mikolon Andrea B. , Gardner Ian A. , Hietala Sharon K. , Hernandez de Anda Jorge , Chamizo Pestaña Elpidio , Hennager Steven G. , Edmondson Anita J. 
Published: December 2019

ABSTRACT

The sensitivities and specificities of 17 antibody detection tests for brucellosis in goats were estimated. Tests evaluated included the U.S. Department of Agriculture (USDA) card test with 8% cell concentration (8%Card), USDA rapid automated presumptive test (RAP), Mexican rose bengal plate tests with 8 and 3% cell concentrations (8%RB and 3%RB), French rose bengal plate test with 4.5% cell concentration (4.5%RB), USDA standard plate test (SPT), USDA buffered acidified plate agglutination test (BAPA), USDA and Mexican rivanol tests (URIV and MRIV), USDA standard tube tests with
Brucella abortus
and
Brucella melitensis
antigens (SATA and SATM), serum enzyme-linked immunosorbent assay (ELISA), USDA cold-fixation complement fixation tests with
B. abortus
and
B. melitensis
antigens (CFA and CFM), USDA and Mexican milk ring tests (UBRT and MBRT), and a milk ELISA. Test sensitivity was evaluated by using two groups of 10 goats experimentally infected with
B. melitensis
or
B. abortus
and monitored for 24 weeks. Specificity was evaluated by using 200 brucellosis-free nonvaccinated goats from 10 California herds. The 3%RB was considered a good screening test because of high sensitivity at week 24 postinfection (90%), ease of performance, and low cost. The cold-fixation CFA and CFM had 100% specificity in the field study and were considered appropriate confirmatory tests. The milk ELISA was significantly more sensitive (
P
< 0.05) than the UBRT and significantly more specific (
P
< 0.05) than the MBRT. The milk ELISA also had the advantage of objectivity and ease of interpretation.