bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of EnterohemorrhagicEscherichia coliHemolysin with Serotypes of Shiga-Like-Toxin-ProducingEscherichia coliof Human and Bovine Origins
Authors: Gyles Carlton , Johnson Roger , Gao Anli , Ziebell Kim , Pierard Denis , Aleksic Stojanka , Boerlin Patrick 
Published: December 2019

ABSTRACTIn this study we investigated whether the enterohemorrhagicEscherichia coli(EHEC) hemolysin geneehxAcould be used as an indicator of pathogenicity in Shiga-like-toxin-producingEscherichia coli(SLTEC) isolates. The isolates in a collection of 770 SLTEC strains of human and bovine origins were assigned to group 1 (230 human and 138 bovine SLTEC isolates belonging to serotypes frequently implicated in human disease), group 2 (85 human and 183 bovine isolates belonging to serotypes less frequently implicated in disease), and group 3 (134 bovine isolates belonging to serotypes not implicated in disease). PCR amplification was used to examine all of the SLTEC isolates for the presence ofehxAand the virulence-associated geneseae,slt-I, andslt-II. The percentages of human isolates in groups 1 and 2 that were positive forehxAwere 89 and 46%, respectively, and the percentages of bovine isolates in groups 1 to 3 that were positive forehxAwere 89, 51, and 52%, respectively. The percentages of human isolates in groups 1 and 2 that were positive foreaewere 92 and 27%, respectively, and the percentages of bovine isolates in groups 1 to 3 that were positive foreaewere 78, 15, and 19%, respectively. The frequencies of bothehxAandeaewere significantly higher for group 1 isolates than for group 2 isolates. The presence of theehxAgene was associated with serotype, as was the presence of theeaegene. Some serotypes, such as O117:H4, lacked botheaeandehxAand have been associated with severe disease, but only infrequently. Theslt-Igenes were more frequent in group 1 isolates than in group 2 isolates, and theslt-IIgenes were more frequent in group 2 isolates than in group 1 isolates. In a second experiment we determined the occurrence of theehxAandsltgenes inE. coliisolated from bovine feces. Fecal samples from 175 animals were streaked onto washed sheep erythrocyte agar plates. EightE. coli-like colonies representing all of the morphological types were transferred to MacConkey agar. A total of 1,080E. coliisolates were examined, and theehxAgene was detected in 12 independent strains, only 3 of which were positive forslt. We concluded that theehxAgene was less correlated with virulence than theeaegene was and that EHEC hemolysin alone has limited value for screening bovine feces for pathogenic SLTEC because of presence of theehxAgene in bovine isolates that are not SLTEC.
Prevalence of
Clostridium botulinum
in Finnish Trout Farms: Pulsed-Field Gel Electrophoresis Typing Reveals Extensive Genetic Diversity among Type E Isolates
Authors: Hielm Sebastian , Björkroth Johanna , Hyytiä Eija , Korkeala Hannu 
Published: December 2019

ABSTRACT

The distribution of
Clostridium botulinum
serotypes A, B, E, and F in Finnish trout farms was examined. A total of 333 samples were tested with a neurotoxin-specific PCR assay.
C. botulinum
type E was found in 68% of the farm sediment samples, in 15% of the fish intestinal samples, and in 5% of the fish skin samples. No other serotypes were found. The spore counts determined by the most-probable-number method were considerably higher for the sediments than for the fish intestines and skin; the average values were 2,020, 166, and 310
C. botulinum
type E spores kg
−1
, respectively. The contamination rates in traditional freshwater ponds and marine net cages were high, but in concrete ponds equipped with sediment suction devices the contamination rates were significantly lower. Pulsed-field gel electrophoresis (PFGE) typing of 42 isolates obtained in this survey and 12 North American reference strains generated 28 pulsotypes upon visual inspection, suggesting that there was extensive genetic diversity and that the discriminatory power of PFGE typing in
C. botulinum
type E was high. A numerical analysis of
Sma
I-
Xma
I macrorestriction profiles confirmed these findings, as it divided the 54 isolates into 15 clusters at a similarity level of 76%. For this material, this level of similarity corresponded to a three-band difference in the macrorestriction profiles, which indicated that there is no genotypic proof of a close epidemiological relationship among the clusters.
Evolution of a Pathway for Chlorobenzene Metabolism Leads to Natural Attenuation in Contaminated Groundwater
Authors: van der Meer Jan Roelof , Werlen Christoph , Nishino Shirley F. , Spain Jim C. 
Published: December 2019

ABSTRACT

Complete metabolism of chlorinated benzenes is not a feature that is generally found in aerobic bacteria but is thought to be due to a novel recombination of two separate gene clusters. Such a recombination could be responsible for adaptation of a natural microbial community in response to contamination with synthetic chemicals. This hypothesis was tested in a chlorobenzene (CB)-contaminated aquifer. CB-degrading bacteria from a contaminated site were characterized for a number of years by examining a combination of growth characteristics and DNA-DNA hybridization, PCR, and DNA sequence data. The genetic information obtained for the CB pathway of the predominant microorganism,
Ralstonia
sp. strain JS705, revealed a unique combination of (partially duplicated) genes for chlorocatechol degradation and genes for a benzene-toluene type of aromatic ring dioxygenase. The organism was detected in CB-polluted groundwater by hybridizing colonies cultivated on low-strength heterotrophic media with probes for the CB pathway. Southern hybridizations performed to determine the organization of the CB pathway genes and the 16S ribosomal DNA indicated that CB-degrading organisms isolated from different wells at the site were identical to JS705. Physiological characterization by the Biolog test system revealed some differences. The genes for the aromatic ring dioxygenase and dihydrodiol dehydrogenase of JS705 were detected in toluene and benzene degraders from the same site. Our results suggest that recent horizontal gene transfer and genetic recombination of existing genes between indigenous microorganisms were the mechanisms for evolution of the catabolic pathway. Evolution of the CB pathway seems to have created the capacity for natural attenuation of CB at the contaminated site.
PCR Detection ofCoxiella burnetiifrom Different Clinical Specimens, Especially Bovine Milk, on the Basis of DNA Preparation with a Silica Matrix
Authors: Lorenz Helga , Jäger Cornelie , Willems Hermann , Baljer Georg 
Published: December 2019

ABSTRACTFor PCR detection ofCoxiella burnetiiin various clinical specimens we developed a sample preparation method in which silica binding of DNA was used. This method was found to be fast, easily performed with large numbers of samples, and equally sensitive for all of the specimens tested (livers, spleens, placentas, heart valves, milk, blood). The DNA preparation method described here can also be used as an initial step in any PCR-based examination of specimens. The procedure was tested with more than 600 milk samples, which were taken from 21 cows that were seropositive forC. burnetiiand reportedly had fertility problems (and therefore were suspected of shedding the agent through milk intermittently or continuously). Of the 21 cows tested, 6 were sheddingC. burnetiithrough milk. Altogether,C. burnetiiDNA was detected in 6% of the samples. There was no correlation between the shedding pattern and the serological results.
rRNA Stability in Heat-Killed and UV-Irradiated Enterotoxigenic
Staphylococcus aureus
and
Escherichia coli
O157:H7
Authors: McKillip John L. , Jaykus Lee-Ann , Drake Maryanne 
Published: December 2019

ABSTRACT

Differentiation of viable cells from nonviable cells is of considerable importance in the development of methods to detect foodborne pathogens. To study the suitability of 16S rRNA as an indicator of cell viability in nucleic acid-based detection assays, we examined rRNA stability in two representative foodborne pathogens,
Escherichia coli
O157:H7 and enterotoxigenic
Staphylococcus aureus
, which were inactivated by extreme heat, moderate heat, and UV irradiation. Cell death under all conditions was confirmed by a failure to grow in brain heart infusion broth after incubation for 48 h at 37°C. rRNA stability was monitored by a Northern blot analysis, and detection was evaluated by using reverse transcription (RT)-PCR performed with two primer sets (which produced 325- and 1,400-bp amplicons). rRNA of neither pathogen was detected by Northern blot analysis and RT-PCR after cells were killed by autoclaving at 121°C for 15 min. In contrast, intact rRNA of both pathogens were detected by Northern blotting and could be amplified by RT-PCR up to 48 h after cells were killed by heat treatment at 80°C and UV irradiation at 254 nm. rRNA was a suitable target molecule for monitoring bacterial viability under extreme heat conditions, but the presence of rRNA was not correlated with viability following moderate heat inactivation or UV irradiation of cells.
Selection and Characterization of Microorganisms Utilizing Thaxtomin A, a Phytotoxin Produced by
Streptomyces scabies
Authors: Doumbou Cyr Lézin , Akimov Vladimir , Beaulieu Carole 
Published: December 2019

ABSTRACT

Thaxtomin A is the main phytotoxin produced by
Streptomyces scabies
, a causal agent of potato scab. Thaxtomin A is a yellow compound composed of 4-nitroindol-3-yl-containing 2,5-dioxopiperazine. A collection of nonpathogenic streptomycetes isolated from potato tubers and microorganisms recovered from a thaxtomin A solution were examined for the ability to grow in the presence of thaxtomin A as a sole carbon or nitrogen source. Three bacterial isolates and two fungal isolates grew in thaxtomin A-containing media. Growth of these organisms resulted in decreases in the optical densities at 400 nm of culture supernatants and in 10% reductions in the thaxtomin A concentration. The fungal isolates were identified as a
Penicillium
sp. isolate and a
Trichoderma
sp. isolate. One bacterial isolate was associated with the species
Ralstonia pickettii
, and the two other bacterial isolates were identified as
Streptomyces
sp. strains. The sequences of the 16S rRNA genes were determined in order to compare thaxtomin A-utilizing actinomycetes to the pathogenic organism
S. scabies
and other
Streptomyces
species. The nucleotide sequences of the γ variable regions of the 16S ribosomal DNA of both thaxtomin A-utilizing actinomycetes were identical to the sequence of
Streptomyces mirabilis
ATCC 27447. When inoculated onto potato tubers, the three thaxtomin A-utilizing bacteria protected growing plants against common scab, but the fungal isolates did not have any protective effect.
Difluoromethane, a New and Improved Inhibitor of Methanotrophy
Authors: Miller Laurence G. , Sasson Caleb , Oremland Ronald S. 
Published: December 2019

ABSTRACT

Difluoromethane (HFC-32; DFM) is compared to acetylene and methyl fluoride as an inhibitor of methanotrophy in cultures and soils. DFM was found to be a reversible inhibitor of CH
4
oxidation by
Methylococcus capsulatus
(Bath). Consumption of CH
4
in soil was blocked by additions of low levels of DFM (0.03 kPa), and this inhibition was reversed by DFM removal. Although a small quantity of DFM was consumed during these incubations, its remaining concentration was sufficiently elevated to sustain inhibition. Methanogenesis in anaerobic soil slurries, including acetoclastic methanogenesis, was unaffected by levels of DFM which inhibit methanotrophy. Low levels of DFM (0.03 kPa) also inhibited nitrification and N
2
O production by soils. DFM is proposed as an improved inhibitor of CH
4
oxidation over acetylene and/or methyl fluoride on the basis of its reversibility, its efficacy at low concentrations, its lack of inhibition of methanogenesis, and its low cost.
Characterization of the Basic Replicon of
Rhodococcus
Plasmid pSOX and Development of a
Rhodococcus-Escherichia coli
Shuttle Vector
Authors: Denis-Larose Claude , Bergeron Hélène , Labbé Diane , Greer Charles W. , Hawari Jalal , Grossman Matthew J. , Sankey Bruce M. , Lau Peter C. K. 
Published: December 2019

ABSTRACT

The replication region of a 100-kb desulfurization plasmid (pSOX) from
Rhodococcus
sp. strain X309 was localized to a 4-kb
Kpn
I fragment, and its sequence was determined. The amino acid sequence of one of the predicted open reading frames (ORFs) was related to the putative replication (Rep) protein sequences of the mycobacterial pLR7 family of plasmids. Three of the five predicted ORF products were identified by radiolabelling with the
Escherichia coli
T7 polymerase/promoter system. In
E. coli
, the Rep protein of pSOX was apparently synthesized in a shortened form, 21.3 kDa instead of the predicted 41.3 kDa, as a result of an internal initiation. This situation is reminescent of that for some bacterial Rep proteins. A shuttle plasmid was constructed with the pSOX origin, pBluescript II KS−, and the chloramphenicol resistance (Cm
r
) gene from pRF29. This new shuttle plasmid was used to demonstrate expression of the
Bacillus subtilis sacB
gene in a strain of
Rhodococcus
, rendering it sensitive to the presence of sucrose.
Identification of a Marine AgarolyticPseudoalteromonasIsolate and Characterization of Its Extracellular Agarase
Authors: Vera Jorge , Alvarez Raul , Murano Erminio , Slebe Juan Carlos , Leon Oscar 
Published: December 2019

ABSTRACTThe phenotypic and agarolytic features of an unidentified marine bacteria that was isolated from the southern Pacific coast was investigated. The strain was gram negative, obligately aerobic, and polarly flagellated. On the basis of several phenotypic characters and a phylogenetic analysis of the genes coding for the 16S rRNA, this strain was identified asPseudoalteromonas antarcticastrain N-1. In solid agar, this isolate produced a diffusible agarase that caused agar softening around the colonies. An extracellular agarase was purified by ammonium sulfate precipitation, gel filtration, and ion-exchange chromatography on DEAE-cellulose. The purified protein was determined to be homogeneous on the basis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and it had a molecular mass of 33 kDa. The enzyme hydrolyzed the β-1,4-glycosydic linkages of agar, yielding neoagarotetraose and neoagarohexaose as the main products, and exhibited maximal activity at pH 7. The enzyme was stable at temperatures up to 30°C, and its activity was not affected by salt concentrations up to 0.5 M NaCl.
Molecular Characterization of Epiphytic Bacterial Communities on Charophycean Green Algae
Authors: Fisher Madeline M. , Wilcox Lee W. , Graham Linda E. 
Published: December 2019

ABSTRACT

Epiphytic bacterial communities within the sheath material of three filamentous green algae,
Desmidium grevillii
,
Hyalotheca dissiliens
, and
Spondylosium pulchrum
(class Charophyceae, order Zygnematales), collected from a
Sphagnum
bog were characterized by PCR amplification, cloning, and sequencing of 16S ribosomal DNA. A total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. By phylogenetic analysis, the cloned sequences were placed into several major lineages of the
Bacteria
domain: the
Flexibacter/Cytophaga/Bacteroides
phylum and the α, β, and γ subdivisions of the phylum
Proteobacteria
. Analysis at the subphylum level revealed that the majority of our sequences were not closely affiliated with those of known, cultured taxa, although the estimated evolutionary distances between our sequences and their nearest neighbors were always less than 0.1 (i.e., greater than 90% similar). This result suggests that the majority of sequences obtained in this study represent as yet phenotypically undescribed bacterial species and that the range of bacterial-algal interactions that occur in nature has not yet been fully described.
Comparison of the BAX for Screening/
E. coli
O157:H7 Method with Conventional Methods for Detection of Extremely Low Levels of
Escherichia coli
O157:H7 in Ground Beef
Authors: Johnson Jennifer L. , Brooke Cheryl L. , Fritschel Scott J. 
Published: December 2019

ABSTRACT

Escherichia coli
O157:H7 is an important food-borne pathogen. Often
E. coli
O157:H7 is difficult to detect, because it is present sporadically at very low levels together with very high levels of competitor organisms which can be difficult to distinguish phenotypically. Cultural methods are time-consuming and give variable results in the detection of
E. coli
O157:H7. This study examined the performance of BAX for Screening/
E. coli
O157:H7, a new rapid method for the detection of
E. coli
O157:H7, against traditional and improved cultural methods and an immunodiffusion assay. All cultural methods demonstrated inadequacy in detecting the presence of
E. coli
O157:H7 in inoculated samples. The limitations of these cultural methods further complicate evaluation of screening methodologies. The BAX for Screening/
E. coli
O157:H7 assay outperformed the other methods, with a detection rate of 96.5%, compared to 39% for the best cultural method and 71.5% for the immunodiffusion method. The BAX for Screening/
E. coli
O157:H7 assay proved to be a rapid, highly sensitive test for the detection of low levels of
E. coli
O157:H7 in ground beef.
Immunomagnetic Separation of
Cryptosporidium parvum
from Source Water Samples of Various Turbidities
Authors: Bukhari Z. , McCuin R. M. , Fricker C. R. , Clancy J. L. 
Published: December 2019

ABSTRACT

Immunomagnetic separation (IMS) procedures which specifically capture
Cryptosporidium
oocysts and have the potential to isolate oocysts from debris have become commercially available. We compared two IMS kits (kit DB [Dynabeads anti-
Cryptosporidium
; product no. 730.01; Dynal A.S., Oslo, Norway] and kit IC1 [Crypto Scan IMS; product no. R10; Clearwater Diagnostics Company, LLC, Portland, Maine]) and a modification of kit IC1 (kit IC2 [Crypto Scan IMS; product no. R10; Clearwater Diagnostics Company, LLC]) at three turbidity levels (50, 500, and 5,000 nephelometric turbidity units [ntu]) by using water matrices obtained from different geographical locations. In deionized water, kit DB yielded recoveries between 68 and 83%, whereas the recoveries obtained with kits IC1 and IC2 were more variable and ranged from 0.2 to 74.5%. In water matrices with turbidity levels up to 500 ntu, the oocyst recoveries were more variable with kit DB; however, the recoveries were similar to those obtained in deionized water. In contrast, there were notable reductions in oocyst recoveries in the turbid matrices with kits IC1 and IC2, and the highest recovery (8.3%) was obtained with a 50-ntu sample. An examination of the effects of age on oocyst recovery with kit DB revealed that oocysts up to 16 weeks old yielded recoveries similar to the recoveries observed with fresh oocysts. These data indicate that all IMS kits do not perform equally well, and it is important to conduct in-house quality assurance work before a commercially available IMS kit is selected to replace flotation procedures for recovery of
Cryptosporidium
oocysts.
Analysis of Subfossil Molecular Remains of Purple Sulfur Bacteria in a Lake Sediment
Authors: Coolen Marco J. L. , Overmann Jörg 
Published: December 2019

ABSTRACT

Molecular remains of purple sulfur bacteria (
Chromatiaceae
) were detected in Holocene sediment layers of a meromictic salt lake (Mahoney Lake, British Columbia, Canada). The carotenoid okenone and bacteriophaeophytin
a
were present in sediments up to 11,000 years old. Okenone is specific for only a few species of
Chromatiaceae
, including
Amoebobacter purpureus
, which presently predominates in the chemocline bacterial community of the lake. With a primer set specific for
Chromatiaceae
in combination with denaturing gradient gel electrophoresis, 16S rRNA gene sequences of four different
Chromatiaceae
species were retrieved from different depths of the sediment. One of the sequences, which originated from a 9,100-year-old sample, was 99.2% identical to the 16S rRNA gene sequence of
A. purpureus
ML1 isolated from the chemocline. Employing primers specific for
A. purpureus
ML1 and dot blot hybridization of the PCR products, the detection limit for
A. purpureus
ML1 DNA could be lowered to 0.004% of the total community DNA. With this approach the DNA of the isolate was detected in 7 of 10 sediment layers, indicating that
A. purpureus
ML1 constituted at least a part of the ancient purple sulfur bacterial community. The concentrations of
A. purpureus
DNA and okenone in the sediment were not correlated, and the ratio of DNA to okenone was much lower in the subfossil sediment layers (2.7 · 10
−6
) than in intact cells (1.4). This indicates that degradation rates are significantly higher for genomic DNA than for hydrocarbon cell constituents, even under anoxic conditions and at the very high sulfide concentrations present in Mahoney Lake.
Inactivation of
Escherichia coli
O157:H7 in Apple Juice by Irradiation
Authors: Buchanan R. L. , Edelson S. G. , Snipes K. , Boyd G. 
Published: December 2019

ABSTRACT

Three strains (932, Ent-C9490, and SEA13B88) of
Escherichia coli
O157:H7 were used to determine the effectiveness of low-dose gamma irradiation for eliminating
E. coli
O157:H7 from apple juice or cider and to characterize the effect of inducing pH-dependent, stationary-phase acid resistance on radiation resistance. The strains were grown in tryptic soy broth with or without 1% dextrose for 18 h to produce cells that were or were not induced to pH-dependent stationary-phase acid resistance. The bacteria were then transferred to clarified apple juice and irradiated at 2°C with a cesium-137 irradiator. Non-acid-adapted cells had radiation
D
values (radiation doses needed to decrease a microbial population by 90%) ranging from 0.12 to 0.21 kGy.
D
values increased to 0.22 to 0.31 kGy for acid-adapted cells. When acid-adapted SEA13B88 cells were tested in five apple juice brands having different levels of suspended solids (absorbances ranging from 0.04 to 2.01 at 550 nm), radiation resistance increased with increasing levels of suspended solids, with
D
values ranging from 0.26 to 0.35 kGy. Based on these results, a dose of 1.8 kGy should be sufficient to achieve the 5
D
inactivation of
E. coli
recommended by the National Advisory Committee for Microbiological Criteria for Foods.