bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription of the SsrAB Regulon Is Repressed by Alkaline pH and Is Independent of PhoPQ and Magnesium Concentration
Authors: Miao Edward A. , Freeman Jeremy A. , Miller Samuel I. 
Published: April 2009

ABSTRACTTheSalmonellapathogenicity island 2 (SPI-2) type III secretion system is expressed by intracellular bacteria and translocates effector proteins across the vacuolar membrane. Signals sensed bySalmonella entericaserovar Typhimurium in the intracellular compartment activate SPI-2 gene expression through the two-component regulatory system SsrAB. The effects of environmental and genetic signals on expression of the SsrAB-regulated genesspH2were examined. SsrAB-dependent activation ofsspH2was detected in the presence of both low and moderate concentrations of magnesium or calcium and at acidic and neutral pHs. The levels of expression were comparable to those detected in bacteria recovered from cultured macrophages. The induction in media at alkaline pHs (pH 7.5 and 8.0) was greatly reduced compared to the induction observed at pH 7.0 or at a lower pH, suggesting that alkaline pH represses SsrAB activation. In addition, the PhoPQ two-component system, which is also activated intracellularly, was not required for activation of SsrAB.
Characterization of the
petI
and
res
Operons of
Acidithiobacillus ferrooxidans
Authors: Levicán Gloria , Bruscella Patrice , Guacunano Maritza , Inostroza Carolina , Bonnefoy Violaine , Holmes David S. , Jedlicki Eugenia 
Published: April 2009

ABSTRACT

DNA sequence analysis and bioinformatic interpretations have identified two adjacent clusters of genes potentially involved in the formation of a bc1 complex and in the maturation of a cytochrome
c
-type protein in two strains (ATCC 19859 and ATCC 33020) of the acidophilic, chemolithoautotrophic bacterium
Acidithiobacillus ferrooxidans
(formerly
Thiobacillus ferrooxidans
). Reverse transcriptase-PCR experiments suggest that the two clusters are organized as operons, and +1 start sites of transcription for the operons have been determined by primer extension experiments. Potential promoters have been identified. The presence of these operons lends support to a recent model of reverse electron flow and is consistent with previous reports of phenotypic switching in this bacterium.
Spectrum of Zygomycete Species Identified in Clinically Significant Specimens in the United States
Authors: Alvarez E. , Sutton D. A. , Cano J. , Fothergill A. W. , Stchigel A. , Rinaldi M. G. , Guarro J. 
Published: April 2009

ABSTRACT

Several members of the order
Mucorales
(subphylum
Mucoromycotina
) are important agents of severe human infections. The identification of these fungi by using standard mycologic methods is often difficult and time consuming. Frequently, the etiological agent in clinical cases is reported either as a
Mucor
sp., which is not the most frequent genus of zygomycetes, or only as a member of the
Mucorales
. For this reason, the actual spectrum of species of zygomycetes and their incidences in the clinical setting is not well known. The goals of this study were to compare the results of the molecular identification of an important set of clinical isolates, received in a mycological reference center from different regions of the United States, with those obtained by using the traditional morphological methods and to determine the spectrum of species involved. We tested 190 isolates morphologically identified as zygomycetes by using sequencing of the internal transcribed spacer (ITS) region of the ribosomal DNA. Molecular identification revealed that
Rhizopus oryzae
represented approximately half (44.7%) of these isolates. The remainder was identified as
Rhizopus microsporus
(22.1%),
Mucor circinelloides
(9.5%),
Mycocladus corymbifer
(formerly
Absidia corymbifera
) (5.3%),
Rhizomucor pusillus
(3.7%),
Cunninghamella bertholletiae
(3.2%),
Mucor indicus
(2.6%),
Cunninghamella echinulata
(1%), and
Apophysomyces elegans
(0.5%). The most common anatomic sites for clinically significant zygomycetes, as determined by isolates sent to the Fungus Testing Laboratory for identification and/or susceptibility testing and included in this study, were the sinuses, lungs, and various cutaneous locations, at 25.8%, 26.8%, and 28%, respectively. These sites represented approximately 80% of the isolates evaluated. A high level of correlation (92.6%) between morphological and molecular identifications was found.
First Spanish Case of Nocardiosis Caused by
Nocardia takedensis
Authors: Betrán A. , Rezusta A. , Lezcano M. A. , Villuendas M. C. , Revillo M. J. , Boiron P. , Rodríguez-Nava V. 
Published: April 2009

ABSTRACT

Nocardia takedensis
is a recently described species isolated from soil. The first clinical isolate in Japan has recently been reported. This report describes the first clinical isolate of
N. takedensis
in Spain from a respiratory specimen.
Fine-Needle Aspiration, an Efficient Sampling Technique for Bacteriological Diagnosis of Nonulcerative Buruli Ulcer
Authors: Eddyani Miriam , Fraga Alexandra G. , Schmitt Fernando , Uwizeye Cécile , Fissette Krista , Johnson Christian , Aguiar Julia , Sopoh Ghislain , Barogui Yves , Meyers Wayne M. , Pedrosa Jorge , Portaels Françoise 
Published: April 2009

ABSTRACTInvasive punch or incisional skin biopsy specimens are currently employed for the bacteriological confirmation of the clinical diagnosis of Buruli ulcer (BU), a cutaneous infectious disease caused byMycobacterium ulcerans. The efficacy of fine-needle aspirates (FNA) using fine-gauge needles (23G by 25 mm) for the laboratory confirmation of BU was compared with that of skin tissue fragments obtained in parallel by excision or punch biopsy. In three BU treatment centers in Benin, both types of diagnostic material were obtained from 33 clinically suspected cases of BU and subjected to the same laboratory analyses: i.e., direct smear examination, IS2404PCR, and in vitro culture. Twenty-three patients, demonstrating 17 ulcerative and 6 nonulcerative lesions, were positive by at least two tests and were therefore confirmed to have active BU. A total of 68 aspirates and 68 parallel tissue specimens were available from these confirmed patients. When comparing the sensitivities of the three confirmation tests between FNA and tissue specimens, the latter yielded more positive results, but only for PCR was this significant. When only nonulcerative BU lesions were considered, however, the sensitivities of the confirmation tests using FNA and tissue specimens were not significantly different. Our results show that the minimally invasive FNA technique offers enough sensitivity to be used for the diagnosis of BU in nonulcerative lesions.
Genetic Relationships Deduced from
emm
and Multilocus Sequence Typing of Invasive
Streptococcus dysgalactiae
subsp.
equisimilis
and
S. canis
Recovered from Isolates Collected in the United States
Authors: Ahmad Yusra , Gertz Robert E. , Li Zhongya , Sakota Varja , Broyles Laura N. , Van Beneden Chris , Facklam Richard , Shewmaker P. Lynn , Reingold Arthur , Farley Monica M. , Beall Bernard W. 
Published: April 2009

ABSTRACT

Beta-hemolytic group C and G streptococci cause a considerable invasive disease burden and sometimes cause disease outbreaks. Little is known about the critical epidemiologic parameter of genetic relatedness between isolates. We determined the
emm
types of 334
Streptococcus dysgalactiae
subsp.
equisimilis
isolates, and attempted
emm
typing of 5
Streptococcus canis
isolates from a recent population-based surveillance for invasive isolates. Thirty-four
emm
types were observed, including one from
S. canis
. We formulated multilocus sequence typing (MLST) primers with six of the seven loci corresponding to the
Streptococcus pyogenes
MLST scheme. We performed MLST with 65 of the 334 surveillance isolates (61
S. dysgalactiae
subsp.
equisimilis
isolates, 4
S. canis
isolates) to represent each
emm
type identified, including 2 to 3 isolates for each of the 25 redundantly represented
emm
types. Forty-one MLST sequence types (STs) were observed. Isolates within 16 redundantly represented
S. dysgalactiae
subsp.
equisimilis emm
types shared identical or nearly identical STs, demonstrating concordance between the
emm
type and genetic relatedness. However, seven STs were each represented by two to four different
emm
types, and 7 of the 10
S. dysgalactiae
subsp.
equisimilis
eBURST groups represented up to six different
emm
types. Thus,
S. dysgalactiae
subsp.
equisimilis
isolates were similar to
S. pyogenes
isolates, in that strains of the same
emm
type were often highly related, but they differed from
S. pyogenes
, in that
S. dysgalactiae
subsp.
equisimilis
strains with identical or closely similar STs often exhibited multiple unrelated
emm
types. The phylogenetic relationships between
S. dysgalactiae
subsp.
equisimilis
and
S. pyogenes
alleles revealed a history of interspecies recombination, with either species often serving as genetic donors. The four
S. canis
isolates shared highly homologous alleles but were unrelated clones without evidence of past recombination with
S. dysgalactiae
subsp.
equisimilis
or
S. pyogenes
.
Multilocus Variable-Number Tandem-Repeat Method for Typing
Salmonella enterica
Serovar Newport
Authors: Davis Margaret A. , Baker Katherine N. K. , Call Douglas R. , Warnick Lorin D. , Soyer Yesim , Wiedmann Martin , Gröhn Yrjö , McDonough Patrick L. , Hancock Dale D. , Besser Thomas E. 
Published: April 2009

ABSTRACT

In recent years, the proportion of
Salmonella enterica
infections represented by
S. enterica
serovar Newport has increased markedly among humans and animals. Multilocus variable-number tandem-repeat analysis (MLVA) has proven to be useful in discriminating other highly clonal
Salmonella
serovars. Here, we report on the development of a highly discriminatory MLVA for
Salmonella
serovar Newport.
Cost-Effective Frozen Master Mix Modification of a Commercial Methicillin-Resistant
Staphylococcus aureus
PCR Assay
Authors: Munson Erik , Block Timothy , Voegeli Janet T. , Hryciuk Jeanne E. , Schell Ronald F. 
Published: April 2009

ABSTRACT

The expense inherent to molecular diagnostics may be an overriding concern for a variety of clinical laboratories in the development of PCR-based methicillin-resistant
Staphylococcus aureus
(MRSA) active surveillance programs. BD GeneOhm MRSA assay master mix was reconstituted, aliquoted into SmartCycler tubes in 25-μl volumes, and frozen at −70°C. One hundred percent of archival nasal swab lysates yielded the expected PCR results when incubated in master mix frozen for 1, 2, 3, and 4 weeks. A 98.8% concordance of the final result was observed upon prospective PCR analysis of 320 clinical lysates utilizing freshly reconstituted master mix and 2-week-frozen master mix. Initial unresolved rates generated by frozen master mix and freshly reconstituted master mix differed by 1.6% (
P
= 0.16). Of 50 MRSA-positive lysates, the titers of 32 (64%) were determined to the same value upon initial tandem frozen master mix and freshly reconstituted master mix utilization; the titers of an additional 14 were determined to the same value upon repeat testing. Frozen master mix maintains potency for at least 4 weeks, facilitating detection of MRSA from nasal swab lysates, and may decrease the amount of unused reagent up to an average of 33%.
Rapid Group-, Serotype-, and Vaccine Strain-Specific Identification of Poliovirus Isolates by Real-Time Reverse Transcription-PCR Using Degenerate Primers and Probes Containing Deoxyinosine Residues
Authors: Kilpatrick David R. , Yang Chen-Fu , Ching Karen , Vincent Annelet , Iber Jane , Campagnoli Ray , Mandelbaum Mark , De Lina , Yang Su-Ju , Nix Allan , Kew Olen M. 
Published: April 2009

ABSTRACT
We have adapted our previously described poliovirus diagnostic reverse transcription-PCR (RT-PCR) assays to a real-time RT-PCR (rRT-PCR) format. Our highly specific assays and rRT-PCR reagents are designed for use in the WHO Global Polio Laboratory Network for rapid and large-scale identification of poliovirus field isolates.
Evaluation of the New Vitek 2 ANC Card for Identification of Medically Relevant Anaerobic Bacteria
Authors: Mory Francine , Alauzet Corentine , Matuszeswski Céline , Riegel Philippe , Lozniewski Alain 
Published: April 2009

ABSTRACT
Of 261 anaerobic clinical isolates tested with the new Vitek 2 ANC card, 257 (98.5%) were correctly identified at the genus level. Among the 251 strains for which identification at the species level is possible with regard to the ANC database, 217 (86.5%) were correctly identified at the species level. Two strains (0.8%) were not identified, and eight were misidentified (3.1%). Of the 21 strains (8.1%) with low-level discrimination results, 14 were correctly identified at the species level by using the recommended additional tests. This system is a satisfactory new automated tool for the rapid identification of most anaerobic bacteria isolated in clinical laboratories.
Detection of
Streptococcus pneumoniae
Strain Cocolonization in the Nasopharynx
Authors: Brugger Silvio D. , Hathaway Lucy J. , Mühlemann Kathrin 
Published: April 2009

ABSTRACT

Colonization with more than one distinct strain of the same species, also termed cocolonization, is a prerequisite for horizontal gene transfer between pneumococcal strains that may lead to change of the capsular serotype. Capsule switch has become an important issue since the introduction of conjugated pneumococcal polysaccharide vaccines. There is, however, a lack of techniques to detect multiple colonization by
S. pneumoniae
strains directly in nasopharyngeal samples. Two hundred eighty-seven nasopharyngeal swabs collected during the prevaccine era within a nationwide surveillance program were analyzed by a novel technique for the detection of cocolonization, based on PCR amplification of a noncoding region adjacent to the pneumolysin gene (
plyNCR
) and restriction fragment length polymorphism (RFLP) analysis. The numbers of strains and their relative abundance in cocolonized samples were determined by terminal RFLP. The pneumococcal carriage rate found by PCR was 51.6%, compared to 40.0% found by culture. Cocolonization was present in 9.5% (10/105) of samples, most (9/10) of which contained two strains in a ratio of between 1:1 and 17:1. Five of the 10 cocolonized samples showed combinations of vaccine types only (
n
= 2) or combinations of nonvaccine types only (
n
= 3). Carriers of multiple pneumococcal strains had received recent antibiotic treatment more often than those colonized with a single strain (33% versus 9%,
P
= 0.025). This new technique allows for the rapid and economical study of pneumococcal cocolonization in nasopharyngeal swabs. It will be valuable for the surveillance of
S. pneumoniae
epidemiology under vaccine selection pressure.
Rapid Variable-Number Tandem-Repeat Genotyping for
Mycobacterium leprae
Clinical Specimens
Authors: Kimura Miyako , Sakamuri Rama Murthy , Groathouse Nathan A. , Rivoire Becky L. , Gingrich David , Krueger-Koplin Susan , Cho Sang-Nae , Brennan Patrick J. , Vissa Varalakshmi 
Published: April 2009

ABSTRACT

Mycobacterium leprae
is the noncultivable pathogen of leprosy. Since the genome sequence of an isolate of
M. leprae
has become available, multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) has been explored as a tool for strain typing and identification of chains of transmission of leprosy. In order to discover VNTRs and develop methods transferable to clinical samples, MLVA was applied to a global collection of
M. leprae
isolates derived from leprosy patients and propagated in armadillo hosts. PCR amplification, agarose gel electrophoresis, and sequencing methods were applied to DNA extracts from these infected armadillo tissues (
n
= 21). We identified polymorphisms in 15 out of 25 short-tandem-repeat (STR) loci previously selected by in silico analyses of the
M. leprae
genome. We then developed multiplex PCR for amplification of these 15 loci in four separate PCRs suitable for fluorescent fragment length analysis and demonstrated STR profiles highly concordant with those from the sequencing methods. Subsequently, we extended this method to DNA extracts from human clinical specimens, such as skin biopsy specimens (
n
= 30). With these techniques, mapping of multiple loci and differentiation of genotypes have been possible using total DNA extracts from limited amounts of clinical samples at a reduced cost and with less time. These practical methods are therefore available and applicable to answer focused epidemiological questions and to allow monitoring of the transmission of
M. leprae
in different countries where leprosy is endemic.
Detection of Plasmid-Mediated Quinolone Resistance Genes in Clinical Isolates of
Enterobacter
spp. in Spain
Authors: Cano M. E. , Rodríguez-Martínez J. M. , Agüero J. , Pascual A. , Calvo J. , García-Lobo J. M. , Velasco C. , Francia M. V. , Martínez-Martínez L. 
Published: April 2009

ABSTRACT

We have studied by PCR and DNA sequencing the presence of the
qnrA, qnrB, qnrS, aac
(
6′
)
-Ib-cr, qepA, intI1
, and IS
CR1
genes in 200 clinical isolates of
Enterobacter cloacae
(
n
= 153) and
E. aerogenes
(
n
= 47) consecutively collected between January 2004 and October 2005 in two hospitals located in Santander (northern Spain) and Seville (southern Spain). Mutations in the quinolone resistance-determining region of
gyrA
and
parC
also were investigated in organisms containing plasmid-mediated quinolone resistance genes. The isolates had different resistant phenotypes, including AmpC hyperproduction, extended-spectrum β-lactamase production, resistance or decreased susceptibility to quinolones, and/or resistance to aminoglycosides. Among the 116
E. cloacae
isolates from Santander,
qnrS1, qnrB5, qnrB2
, and
aac
(
6′
)
-Ib-cr
were detected in 22 (19%), 1 (0.9%), 1 (0.9%), and 3 (2.6%) isolates, respectively. Twenty-one, 17, and 2
qnrS1
-positive isolates also contained
bla
LAP-1
,
intI1
, and IS
CR1
, respectively. A
qnrB7
-like gene was detected in one
E. aerogenes
isolate from Santander. No plasmid-mediated quinolone resistance gene was detected in the isolates from Seville. The
qnrS1
-containing isolates corresponded to four pulsed-field gel electrophoresis patterns and showed various levels of resistance to quinolones. Six isolates were susceptible to nalidixic acid and presented reduced susceptibility to ciprofloxacin. The
qnrS1
gene was contained in a conjugative plasmid of ca. 110 kb, and when the plasmid was transferred to recipient strains that did not have a specific mechanism of quinolone resistance, the ciprofloxacin MICs ranged from 0.047 to 0.125 μg/ml.
Cutaneous Infection Caused by
Macrophomina phaseolina
in a Child with Acute Myeloid Leukemia
Authors: Srinivasan Ashok , Wickes Brian L. , Romanelli Anna M. , Debelenko Larisa , Rubnitz Jeffrey E. , Sutton Deanna A. , Thompson Elizabeth H. , Fothergill Annette W. , Rinaldi Michael G. , Hayden Randall T. , Shenep Jerry L. 
Published: April 2009

ABSTRACT

We report a case of
Macrophomina phaseolina
skin infection in an immunocompromised child with acute myeloid leukemia, which was treated successfully with posaconazole without recurrence after a hematopoietic stem cell transplant. The fungus was identified by DNA sequencing using both the internal transcribed spacer and D1/D2 region of the 28S ribosomal DNA gene.
No Correlation between Giant Cell Arteritis andChlamydia pneumoniaeInfection: Investigation of 189 Patients by Standard and Improved PCR Methods
Authors: Njau Florence , Ness Thomas , Wittkop Ulrike , Pancratz Thorsten , Eickhoff Meike , Hudson Alan P. , Haller Hermann , Wagner Annette D. 
Published: April 2009

ABSTRACTA total of 189 temporal artery biopsy samples from giant cell arteritis (GCA) patients were investigated using sensitive PCR targetingChlamydia pneumoniae. Chlamydial DNA was detected in 17 samples, 11 of which were positive for chlamydial antigens. Our data did not reveal strong evidence thatC. pneumoniaeplays an important role in the pathogenesis of GCA.
Pulmonary Disease Due to
Mycobacterium arosiense
, an Easily Misidentified Pathogenic Novel Mycobacterium
Authors: Tortoli Enrico , Adriani Beatrice , Baruzzo Serena , Degl'Innocenti Roberto , Galanti Irene , Lauria Stefania , Mariottini Alessandro , Pascarella Michela 
Published: April 2009

ABSTRACT

Mycobacterium arosiense
is a newly described species. After noticing it was misidentified as
Mycobacterium intracellulare
by the commercial identification system GenoType CM (Hein, Nehren, Germany), we detected 4 such strains among 33 that were previously misidentified as
M. intracellulare
. Three more strains were found among unidentified mycobacteria not tested previously with GenoType. The first case of pulmonary disease due to
M. arosiense
is reported here, and the novel species, of which so far only one strain had been investigated, is further characterized.
Activation of the PI3K/Akt Pathway Early during Vaccinia and Cowpox Virus Infections Is Required for both Host Survival and Viral Replication
Authors: Soares Jamária A. P. , Leite Flávia G. G. , Andrade Luciana G. , Torres Alice A. , De Sousa Lirlândia P. , Barcelos Lucíola S. , Teixeira Mauro M. , Ferreira Paulo C. P. , Kroon Erna G. , Souto-Padrón Thaís , Bonjardim Cláudio A. 
Published: April 2009

ABSTRACT
Viral manipulation of the transduction pathways associated with key cellular functions such as actin remodeling, microtubule stabilization, and survival may favor a productive viral infection. Here we show that consistent with the vaccinia virus (VACV) and cowpox virus (CPXV) requirement for cytoskeleton alterations early during the infection cycle, PBK/Akt was phosphorylated at S473 [Akt(S473-P)], a modification associated with the mammalian target of rapamycin complex 2 (mTORC2), which was paralleled by phosphorylation at T308 [Akt(T308-P)] by PI3K/PDK1, which is required for host survival. Notably, while VACV stimulated Akt(S473-P/T308-P) at early (1 h postinfection [p.i.]) and late (24 h p.i.) times during the infective cycle, CPXV stimulated Akt at early times only. Pharmacological and genetic inhibition of PI3K (LY294002) or Akt (Akt-X and a dominant-negative form of Akt-K179M) resulted in a significant decline in virus yield (from 80% to ≥90%). This decline was secondary to the inhibition of late viral gene expression, which in turn led to an arrest of virion morphogenesis at the immature-virion stage of the viral growth cycle. Furthermore, the cleavage of both caspase-3 and poly(ADP-ribose) polymerase and terminal deoxynucleotidyl transferase-mediated deoxyuridine nick end labeling assays confirmed that permissive, spontaneously immortalized cells such as A31 cells and mouse embryonic fibroblasts (MEFs) underwent apoptosis upon orthopoxvirus infection plus LY294002 treatment. Thus, in A31 cells and MEFs, early viral receptor-mediated signals transmitted via the PI3K/Akt pathway are required and precede the expression of viral antiapoptotic genes. Additionally, the inhibition of these signals resulted in the apoptosis of the infected cells and a significant decline in viral titers.
Detection of Nonstructural Protein 6 in Murine Coronavirus-Infected Cells and Analysis of the Transmembrane Topology by Using Bioinformatics and Molecular Approaches
Authors: Baliji Surendranath , Cammer Stephen A. , Sobral Bruno , Baker Susan C. 
Published: April 2009

ABSTRACT
Coronaviruses encode large replicase polyproteins which are proteolytically processed by viral proteases to generate mature nonstructural proteins (nsps) that form the viral replication complex. Mouse hepatitis virus (MHV) replicase products nsp3, nsp4, and nsp6 are predicted to act as membrane anchors during assembly of the viral replication complexes. We report the first antibody-mediated Western blot detection of nsp6 from MHV-infected cells. The nsp6-specific peptide antiserum detected the replicase intermediate p150 (nsp4 to nsp11) and two nsp6 products of approximately 23 and 25 kDa. Analysis of nsp6 transmembrane topology revealed six membrane-spanning segments and a conserved hydrophobic domain in the C-terminal cytosolic tail.