bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diverse Enterotoxin Gene Profiles among Clonal Complexes of
Staphylococcus aureus
Isolates from the Bronx, New York
Authors: Varshney Avanish K. , Mediavilla José R. , Robiou Natalie , Guh Alice , Wang Xiabo , Gialanella Philip , Levi Michael H. , Kreiswirth Barry N. , Fries Bettina C. 
Published: September 2009

ABSTRACT

Staphylococcal
enterotoxins (SE) can cause toxin-mediated disease, and those that function as superantigens are implicated in the pathogenesis of allergic diseases. The prevalence of 19 enterotoxin genes was determined by PCR in clinical
S. aureus
strains derived from wounds (108) and blood (99). We performed
spa
typing and multilocus sequence typing (MLST) to determine clonal origin, and for selected strains staphylococcal enterotoxin B (SEB) production was measured by enzyme-linked immunosorbent assay. Strains carried a median of five SE genes. For most SE genes, the prevalence rates among methicillin-resistant and methicillin-sensitive
S. aureus
isolates, as well as wound- and blood-derived isolates, did not differ. At least one SE gene was detected in all except two
S. aureus
isolates (>99%). Complete
egc
clusters were found in only 11% of
S. aureus
isolates, whereas the combination of
sed
,
sej
, and
ser
was detected in 24% of clinical strains.
S. aureus
strains exhibited distinct combinations of SE genes, even if their pulsed-field gel electrophoresis and MLST patterns demonstrated clonality. USA300 strains also showed considerable variability in SE content, although they contained a lower number of SE genes (mean, 3). By contrast, SE content was unchanged in five pairs of serial isolates. SEB production by individual strains varied up to 200-fold, and even up to 15-fold in a pair of serial isolates. In conclusion, our results illustrate the genetic diversity of
S. aureus
strains with respect to enterotoxin genes and suggest that horizontal transfer of mobile genetic elements encoding virulence genes occurs frequently.
Pathotype and Antibiotic Resistance Gene Distributions of
Escherichia coli
Isolates from Broiler Chickens Raised on Antimicrobial-Supplemented Diets
Authors: Bonnet Claudie , Diarrassouba Fatoumata , Brousseau Roland , Masson Luke , Topp Edward , Diarra Moussa S. 
Published: September 2009

ABSTRACT

The impact of feed supplementation with bambermycin, monensin, narasin, virginiamycin, chlortetracycline, penicillin, salinomycin, and bacitracin on the distribution of
Escherichia coli
pathotypes in broiler chickens was investigated using an
E. coli
virulence DNA microarray. Among 256
E. coli
isolates examined, 59 (23%) were classified as potentially extraintestinal pathogenic
E. coli
(ExPEC), while 197 (77%) were considered commensal. Except for chlortetracycline treatment, the pathotype distribution was not significantly different among treatments (
P
> 0.05). Within the 59 ExPEC isolates, 44 (75%) were determined to be potentially avian pathogenic
E. coli
(APEC), with the remaining 15 (25%) considered potentially “other” ExPEC isolates. The distribution within phylogenetic groups showed that 52 (88%) of the ExPEC isolates belonged to groups B2 and D, with the majority of APEC isolates classified as group D and most commensal isolates (170, 86%) as group A or B1. Indirect assessment of the presence of the virulence plasmid pAPEC-O2-ColV showed a strong association of the plasmid with APEC isolates. Among the 256 isolates, 224 (88%) possessed at least one antimicrobial resistance gene, with nearly half (107, 42%) showing multiple resistance genes. The majority of resistance genes were distributed among commensal isolates. Considering that the simultaneous detection of antimicrobial resistance
tet
(A),
sulI
, and
bla
TEM
genes and the integron class I indicated a potential presence of the resistance pAPEC-O2-R plasmid, the results revealed that 35 (14%) of the isolates, all commensals, possessed this multigene resistance plasmid. The virulence plasmid was never found in combination with the antimicrobial resistance plasmid. The presence of the ColV plasmid or the combination of
iss
and
tsh
genes in the majority of APEC isolates supports the notion that when found together, the plasmid,
iss
, and
tsh
serve as good markers for APEC. These data indicate that different resistant
E. coli
pathotypes can be found in broiler chickens and that the distribution of such pathotypes and certain virulence determinants could be modulated by antimicrobial agent feed supplementation.
Cryptosporidium
Propidium Monoazide-PCR, a Molecular Biology-Based Technique for Genotyping of Viable
Cryptosporidium
Oocysts
Authors: Brescia Cristin C. , Griffin Shannon M. , Ware Michael W. , Varughese Eunice A. , Egorov Andrey I. , Villegas Eric N. 
Published: September 2009

ABSTRACT

Cryptosporidium
is an important waterborne protozoan parasite that can cause severe diarrhea and death in the immunocompromised. The current methods used to monitor for
Cryptosporidium
oocysts in water are the microscopy-based USEPA methods 1622 and 1623. These methods assess total levels of oocysts in source waters, but do not determine oocyst viability or genotype. Recently, propidium monoazide (PMA) has been used in conjunction with molecular diagnostic tools to identify species and assess the viability of bacteria. The goal of this study was the development of a
Cryptosporidium
PMA-PCR (CryptoPMA-PCR) assay that includes PMA treatment prior to PCR analysis in order to prevent the amplification of DNA from dead oocysts. The results demonstrated that PMA penetrates only dead oocysts and blocks amplification of their DNA. The CryptoPMA-PCR assay can also specifically detect live oocysts within a mixed population of live and dead oocysts. More importantly, live oocysts, not dead oocysts, were detected in raw waste or surface water samples spiked with
Cryptosporidium
oocysts. This proof-of-concept study is the first to demonstrate the use of PMA for pre-PCR treatment of
Cryptosporidium
oocysts. The CryptoPMA-PCR assay is an attractive approach to specifically detect and genotype viable
Cryptosporidium
oocysts in the water, which is critical for human health risk assessment.
Effect of Cinnamon Oil on
icaA
Expression and Biofilm Formation by
Staphylococcus epidermidis
Authors: Nuryastuti Titik , van der Mei Henny C. , Busscher Henk J. , Iravati Susi , Aman Abu T. , Krom Bastiaan P. 
Published: September 2009

ABSTRACT

Staphylococcus epidermidis
is notorious for its biofilm formation on medical devices, and novel approaches to prevent and kill
S. epidermidis
biofilms are desired. In this study, the effect of cinnamon oil on planktonic and biofilm cultures of clinical
S. epidermidis
isolates was evaluated. Initially, susceptibility to cinnamon oil in planktonic cultures was compared to the commonly used antimicrobial agents chlorhexidine, triclosan, and gentamicin. The MIC of cinnamon oil, defined as the lowest concentration able to inhibit visible microbial growth, and the minimal bactericidal concentration, the lowest concentration required to kill 99.9% of the bacteria, were determined using the broth microdilution method and plating on agar. A checkerboard assay was used to evaluate the possible synergy between cinnamon oil and the other antimicrobial agents. The effect of cinnamon oil on biofilm growth was studied in 96-well plates and with confocal laser-scanning microscopy (CLSM). Biofilm susceptibility was determined using a metabolic 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay. Real-time PCR analysis was performed to determine the effect of sub-MIC concentrations of cinnamon oil on expression of the biofilm-related gene,
icaA
. Cinnamon oil showed antimicrobial activity against both planktonic and biofilm cultures of clinical
S. epidermidis
strains. There was only a small difference between planktonic and biofilm MICs, ranging from 0.5 to 1% and 1 to 2%, respectively. CLSM images indicated that cinnamon oil is able to detach and kill existing biofilms. Thus, cinnamon oil is an effective antimicrobial agent to combat
S. epidermidis
biofilms.
Insufficiency of Copper Ion Homeostasis Causes Freeze-Thaw Injury of Yeast Cells as Revealed by Indirect Gene Expression Analysis
Authors: Takahashi Shunsuke , Ando Akira , Takagi Hiroshi , Shima Jun 
Published: September 2009

ABSTRACT

Saccharomyces cerevisiae
is exposed to freeze-thaw stress in commercial processes, including frozen dough baking. Cell viability and fermentation activity after a freeze-thaw cycle were dramatically decreased due to freeze-thaw injury. Because this type of injury involves complex phenomena, the injury mechanisms are not fully understood. We examined freeze-thaw injury by indirect gene expression analysis during postthaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that genes involved in the homeostasis of metal ions were frequently contained in genes that were upregulated, depending on the freezing period. We assessed the phenotype of deletion mutants of the metal ion homeostasis genes that exhibited freezing period-dependent upregulation and found that the strains with deletion of the
MAC1
and
CTR1
genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. We found that supplementation with copper ions during postthaw incubation increased intracellular superoxide dismutase activity and intracellular levels of reactive oxygen species were decreased. Moreover, cell viability was increased by supplementation with copper ions. These results suggest that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury.
Dominant Bacteria and Biomass in the Kuytun 51 Glacier
Authors: Xiang Shu-Rong , Shang Tian-Cui , Chen Yong , Jing Ze-Fan , Yao Tandong 
Published: September 2009

ABSTRACT

Dominant bacteria in the different habitats in the Kuytun 51 Glacier were investigated using a 16S rRNA gene clone library sequencing technique. Results showed diverse bacteria on the glacial surface, with the dominant phyla being
Proteobacteria
,
Cyanobacteria
, and
Bacteroidetes.
UniFrac data showed distinct community patterns between the Kuytun and Himalayan Rongbuk glaciers.
Engineering of
Bacillus subtilis
168 for Increased Nisin Resistance
Authors: Hansen Mette E. , Wangari Romilda , Hansen Egon B. , Mijakovic Ivan , Jensen Peter R. 
Published: September 2009

ABSTRACT

Nisin is a natural bacteriocin produced commercially by
Lactococcus lactis
and widely used in the food industry as a preservative because of its broad host spectrum. Despite the low productivity and troublesome fermentation of
L. lactis
, no alternative cost-effective host has yet been found.
Bacillus subtilis
had been suggested as a potential host for the biosynthesis of nisin but was discarded due to its sensitivity to the lethal action of nisin. In this study, we have reevaluated the potential of
B. subtilis
as a host organism for the heterologous production of nisin. We applied transcriptome and proteome analyses of
B. subtilis
and identified eight genes upregulated in the presence of nisin. We demonstrated that the overexpression of some of these genes boosts the natural defenses of
B. subtilis
, which allows it to sustain higher levels of nisin in the medium. We also attempted to overcome the nisin sensitivity of
B. subtilis
by introducing the nisin resistance genes
nisFEG
and
nisI
from
L. lactis
under the control of a synthetic promoter library.
Correlation of Methane Production and Functional Gene Transcriptional Activity in a Peat Soil
Authors: Freitag Thomas E. , Prosser James I. 
Published: September 2009

ABSTRACT

The transcription dynamics of subunit A of the key gene in methanogenesis (methyl coenzyme M reductase;
mcrA
) was studied to evaluate the relationship between process rate (methanogenesis) and gene transcription dynamics in a peat soil ecosystem. Soil methanogen process rates were determined during incubation of peat slurries at temperatures from 4 to 37°C, and real-time quantitative PCR was applied to quantify the abundances of
mcrA
genes and transcripts; corresponding transcriptional dynamics were calculated from
mcrA
transcript/gene ratios. Internal standards suggested unbiased recovery of mRNA abundances in comparison to DNA levels. In comparison to those in pure-culture studies,
mcrA
transcript/gene ratios indicated underestimation by 1 order of magnitude, possibly due to high proportions of inactive or dead methanogens. Methane production rates were temperature dependent, with maxima at 25°C, but changes in abundance and transcription of the
mcrA
gene showed no correlation with temperature. However,
mcrA
transcript/gene ratios correlated weakly (regression coefficient = 0.76) with rates of methanogenesis. Methanogen process rates increased over 3 orders of magnitude, while the corresponding maximum transcript/gene ratio increase was only 18-fold.
mcrA
transcript dynamics suggested steady-state expression in peat soil after incubation for 24 and 48 h, similar to that in stationary-phase cultures.
mcrA
transcript/gene ratios are therefore potential in situ indicators of methanogen process rate changes in complex soil systems.
Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments
Authors: Futagami Taiki , Morono Yuki , Terada Takeshi , Kaksonen Anna H. , Inagaki Fumio 
Published: September 2009

ABSTRACT

Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous (
rdhA
) genes in marine subsurface sediments. A total of 32 putative
rdhA
phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem.
Comparison and Utilization of Repetitive-Element PCR Techniques for Typing
Lactobacillus
Isolates from the Chicken Gastrointestinal Tract
Authors: Stephenson David P. , Moore Robert J. , Allison Gwen E. 
Published: September 2009

ABSTRACT

Three repetitive-element PCR techniques were evaluated for the ability to type strains of
Lactobacillus
species commonly identified in the chicken gastrointestinal tract. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) produced species- and strain-specific profiles for
Lactobacillus crispatus
,
Lactobacillus gallinarum
,
Lactobacillus johnsonii
, and
Lactobacillus reuteri
isolates. The technique typed strains within these species equally as well as pulsed-field gel electrophoresis. DNA concentration and quality did not affect the ERIC-PCR profiles, indicating that this method, unlike other high-resolution methods, can be adapted to high-throughput analysis of isolates. Subsequently, ERIC-PCR was used to type
Lactobacillus
species diversity of a large collection of isolates derived from chickens grown under commercial and necrotic enteritis disease induction conditions. This study has illustrated, for the first time, that there is great strain diversity within each
Lactobacillus
species present and has revealed that chickens raised under commercial conditions harbor greater species and strain diversity than chickens raised under necrotic enteritis disease induction conditions.
Rapid Identification of
Vibrio parahaemolyticus
by Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Hazen Tracy H. , Martinez Robert J. , Chen Yanfeng , Lafon Patricia C. , Garrett Nancy M. , Parsons Michele B. , Bopp Cheryl A. , Sullards M. Cameron , Sobecky Patricia A. 
Published: September 2009

ABSTRACT

Vibrio parahaemolyticus
is a pathogenic marine bacterium that is the main causative agent of bacterial seafood-borne gastroenteritis in the United States. An increase in the frequency of
V. parahaemolyticus
-related infections during the last decade has been attributed to the emergence of an O3:K6 pandemic clone in 1995. The diversity of the O3:K6 pandemic clone and its serovariants has been examined using multiple molecular techniques including multilocus sequence analysis, pulsed-field gel electrophoresis, and group-specific PCR analysis. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a powerful tool for rapidly distinguishing between related bacterial species. In the current study, we demonstrate the development of a whole-cell MALDI-TOF MS method for the distinction of
V. parahaemolyticus
from other
Vibrio
spp. We identified 30 peaks that were present only in the spectra of the
V. parahaemolyticus
strains examined in this study that may be developed as MALDI-TOF MS biomarkers for identification of
V. parahaemolyticus
. We detected variation in the MALDI-TOF spectra of
V. parahaemolyticus
strains isolated from different geographical locations and at different times. The MALDI-TOF MS spectra of the
V. parahaemolyticus
strains examined were distinct from those of the other
Vibrio
species examined including the closely related
V. alginolyticus
,
V. harveyi
, and
V. campbellii
. The results of this study demonstrate the first use of whole-cell MALDI-TOF MS analysis for the rapid identification of
V. parahaemolyticus
.
Microhabitats within Venomous Cone Snails Contain Diverse Actinobacteria
Authors: Peraud Olivier , Biggs Jason S. , Hughen Ronald W. , Light Alan R. , Concepcion Gisela P. , Olivera Baldomero M. , Schmidt Eric W. 
Published: September 2009

ABSTRACT
Actinomycetes can be symbionts in diverse organisms, including both plants and animals. Some actinomycetes benefit their host by producing small molecule secondary metabolites; the resulting symbioses are often developmentally complex. Actinomycetes associated with three cone snails were studied. Cone snails are venomous tropical marine gastropods which have been extensively examined because of their production of peptide-based neurological toxins, but no microbiological studies have been reported on these organisms. A microhabitat approach was used in which dissected tissue from each snail was treated as an individual sample in order to explore bacteria in the tissues separately. Our results revealed a diverse, novel, and highly culturable cone snail-associated actinomycete community, with some isolates showing promising bioactivity in a neurological assay. This suggests that cone snails may represent an underexplored reservoir of novel actinomycetes of potential interest for drug discovery.
Diminished Exoproteome of
Frankia
spp. in Culture and Symbiosis
Authors: Mastronunzio J. E. , Huang Y. , Benson D. R. 
Published: September 2009

ABSTRACT

Frankia
species are the most geographically widespread gram-positive plant symbionts, carrying out N
2
fixation in root nodules of trees and woody shrubs called actinorhizal plants. Taking advantage of the sequencing of three
Frankia
genomes, proteomics techniques were used to investigate the population of extracellular proteins (the exoproteome) from
Frankia
, some of which potentially mediate host-microbe interactions. Initial two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of culture supernatants indicated that cytoplasmic proteins appeared in supernatants as cells aged, likely because older hyphae lyse in this slow-growing filamentous actinomycete. Using liquid chromatography coupled to tandem mass spectrometry to identify peptides, 38 proteins were identified in the culture supernatant of
Frankia
sp. strain CcI3, but only three had predicted export signal peptides. In symbiotic cells, 42 signal peptide-containing proteins were detected from strain CcI3 in
Casuarina cunninghamiana
and
Casuarina glauca
root nodules, while 73 and 53 putative secreted proteins containing signal peptides were identified from
Frankia
strains in field-collected root nodules of
Alnus incana
and
Elaeagnus angustifolia
, respectively. Solute-binding proteins were the most commonly identified secreted proteins in symbiosis, particularly those predicted to bind branched-chain amino acids and peptides. These direct proteomics results complement a previous bioinformatics study that predicted few secreted hydrolytic enzymes in the
Frankia
proteome and provide direct evidence that the symbiosis succeeds partly, if not largely, because of a benign relationship.
Combination of Chromogenic Differential Medium and
estA
-Specific PCR for Isolation and Detection of Phytopathogenic
Xanthomonas
spp
Authors: Lee Yung-An , Sung Ai-Ning , Liu Tzu-Fen , Lee Yung-Shan 
Published: September 2009

ABSTRACT

A xanthomonad differential medium (designated Xan-D medium) was developed, on which streaks and colonies of xanthomonads, including 13 species of the genus
Xanthomonas
, turned wet-shining yellow-green and were surrounded with a smaller milky zone and a bigger clear zone in 3 to 4 days. The characteristics could easily be differentiated from those of yellow nonxanthomonads and other bacteria. The mechanism of color change and formation of a milky zone on the medium are mainly due to the Tween 80 hydrolytic capacity of xanthomonads. The gene,
estA
, responsible for Tween 80 hydrolysis was cloned and expressed in
Escherichia coli
, which acquired a capacity to hydrolyze Tween 80 and could turn green and form a milky zone on the Xan-D medium. The nucleotide sequence of
estA
is highly conserved in the xanthomonads, and the sequence was used to design a specific PCR primer set. The PCR amplification using the primer set amplified a 777-bp specific DNA fragment for all xanthomonad strains tested. The Xan-D medium was used to isolate and differentiate
Xanthomonas campestris
pv. campestris from naturally infected cabbages with black rot symptoms for a rapid diagnosis. All isolated
X. campestris
pv. campestris strains developed characteristic colonies and were positive in the PCR with the
estA
primer set. The Xan-D medium was further amended with antibiotics and successfully used for the detection of viable
X. campestris
pv. campestris cells from plant seeds. Although some yellow nonxanthomonads and other saprophytic bacteria from plant seeds could still grow on the medium, they did not interfere with the color development of
X. campestris
pv. campestris. However,
Stenotrophomonas maltophilia
, which is closely related to xanthomonads, existing in a seed lot could also develop yellow-green color but had different colony morphology and was negative in the PCR with the
estA
primer set. Accordingly, the combination of the Xan-D medium with the
estA
-specific PCR is a useful and reliable method for the isolation and detection of viable xanthomonad cells from plant materials.