bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Active Bacterial Communities before and after Dredging of Highly Polluted Baltic Sea Sediments
Authors: Edlund Anna , Jansson Janet K. 
Published: October 2006

ABSTRACT

Bacteria residing in sediments have key functions in the marine food web. However, it has been difficult to correlate the identity and activity of bacteria in sediments due to lack of appropriate methods beyond cultivation-based techniques. Our aim was to use a combination of molecular approaches, bromodeoxyuridine incorporation and immunocapture, terminal restriction fragment length polymorphism, and cloning and sequencing of 16S rRNA genes to assess the composition of growing bacteria in Baltic Sea sediments. The study site was a highly polluted area off the Swedish coast. The sediments were sampled in two consecutive years, before and after remediation, by dredging of the top sediments. Levels of polyaromatic hydrocarbons (PAHs), mercury, and polychlorinated biphenyls were dramatically reduced as a result of the cleanup project. The compositions of growing members of the communities were significantly different at the two sampling periods. In particular, members from the class
Deltaproteobacteria
and genus
Spirochaeta
were more dominant before dredging, but members of the classes
Gammaproteobacteria
and the
Flavobacteria
represented the most dominant growing populations after dredging. We also cultivated isolates from the polluted sediments that could transform the model PAH compound, phenanthrene. Some of these isolates were confirmed as dominant growing populations by the molecular methods as well. This suite of methods enabled us to link the identity and activity of the members of the sediment communities.
Response of the Microaerophilic
Bifidobacterium
Species,
B. boum
and
B. thermophilum
, to Oxygen
Authors: Kawasaki Shinji , Mimura Tsuyoshi , Satoh Takumi , Takeda Kouji , Niimura Youichi 
Published: October 2006

ABSTRACT

We investigated the effects of O
2
on
Bifidobacterium
species using liquid shaking cultures under various O
2
concentrations. Although most of the
Bifidobacterium
species we selected showed O
2
sensitivity, two species,
B. boum
and
B. thermophilum
, demonstrated microaerophilic profiles. The growth of
B. bifidum
and
B. longum
was inhibited under high-O
2
conditions accompanied by the accumulation of H
2
O
2
in the medium, and growth was restored by adding catalase to the medium.
B. boum
and
B. thermophilum
grew well even under 20% O
2
conditions without H
2
O
2
accumulation, and growth was stimulated compared to anoxic growth. H
2
O-forming NADH oxidase activities were detected dominantly in cell extracts of
B. boum
and
B. thermophilum
under acidic reaction conditions (pH 5.0 to 6.0).
Novel Method To Identify Source-Associated Phylogenetic Clustering Shows thatListeria monocytogenesIncludes Niche-Adapted Clonal Groups with Distinct Ecological Preferences
Authors: Nightingale K. K. , Lyles K. , Ayodele M. , Jalan P. , Nielsen R. , Wiedmann M. 
Published: October 2006

ABSTRACTWhile phylogenetic and cluster analyses are often used to define clonal groups within bacterial species, the identification of clonal groups that are associated with specific ecological niches or host species remains a challenge. We usedListeria monocytogenes, which causes invasive disease in humans and different animal species and which can be isolated from a number of environments including food, as a model organism to develop and implement a two-step statistical approach to the identification of phylogenetic clades that are significantly associated with different source populations, including humans, animals, and food. If the null hypothesis that the genetic distances for isolates within and between source populations are identical can be rejected (SourceCluster test), then particular clades in the phylogenetic tree with significant overrepresentation of sequences from a given source population are identified (TreeStats test). Analysis of sequence data for 120L. monocytogenesisolates revealed evidence of clustering between isolates from the same source, based on the phylogenies inferred fromactAandinlA(P= 0.02 andP= 0.07, respectively; SourceCluster test). Overall, the TreeStats test identified 10 clades with significant (P< 0.05) or marginally significant (P< 0.10) associations with defined sources, including human-, animal-, and food-associated clusters. Epidemiological and virulence phenotype data supported the fact that the source-associated clonal groups identified here are biologically valid. Overall, our data show that (i) the SourceCluster and TreeStats tests can identify biologically meaningful source-associated phylogenetic clusters and (ii)L. monocytogenesincludes clonal groups that have adapted to infect specific host species or colonize nonhost environments.
Use of PCR and Reverse Line Blot Hybridization Macroarray Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences for Rapid Identification of 34
Mycobacterium
Species
Authors: Xiong Likuan , Kong Fanrong , Yang Yingzhou , Cheng Jinquan , Gilbert Gwendolyn L. 
Published: October 2006

ABSTRACT

The aim of this study was to develop a PCR and reverse line blot hybridization (PCR-RLB) macroarray assay based on 16S-23S rRNA gene internal transcribed spacer sequences for the identification and differentiation of 34 mycobacterial species or subspecies. The performance of the PCR-RLB assay was assessed and validated by using 78 reference strains belonging to 55
Mycobacterium
species, 219 clinical isolates which had been identified as mycobacteria by high-performance liquid chromatography or gas chromatography, three skin biopsy specimens from patients with suspected leprosy which had been shown to contain acid-fast bacilli, and isolates of 14 nonmycobacterial species. All mycobacteria were amplified in the PCR and hybridized with a genus-specific probe (probe MYC). The 34 species-specific probes designed in this study hybridized only with the corresponding
Mycobacterium
species. The mycobacterial PCR-RLB assay is an efficient tool for the identification of clinical isolates of mycobacteria; it can reliably identify mixed mycobacterial cultures and
M. leprae
in skin biopsy specimens.
Preparation of His-Tagged Armored RNA Phage Particles as a Control for Real-Time Reverse Transcription-PCR Detection of Severe Acute Respiratory Syndrome Coronavirus
Authors: Cheng Yangjian , Niu Jianjun , Zhang Yongyou , Huang Jianwei , Li Qingge 
Published: October 2006

ABSTRACTArmored RNA has been increasingly used as both an external and internal positive control in nucleic acid-based assays for RNA virus. In order to facilitate armored RNA purification, a His6tag was introduced into the loop region of the MS2 coat protein, which allows the exposure of multiple His tags on the surface during armored RNA assembly. The His-tagged armored RNA particles were purified to homogeneity and verified to be free of DNA contamination in a single run of affinity chromatography. A fragment of severe acute respiratory syndrome coronavirus (SARS-CoV) genome targeted for SARS-CoV detection was chosen for an external positive control preparation. A plant-specific gene sequence was chosen for a universal noncompetitive internal positive control preparation. Both controls were purified by Co2+affinity chromatography and were included in a real-time reverse transcription-PCR assay for SARS-CoV. The noncompetitive internal positive control can be added to clinical samples before RNA extraction and enables the identification of potential inhibitive effects without interfering with target amplification. The external control could be used for the quantification of viral loads in clinical samples.
Comparison of Subtyping Methods for Differentiating
Salmonella enterica
Serovar Typhimurium Isolates Obtained from Food Animal Sources
Authors: Foley Steven L. , White David G. , McDermott Patrick F. , Walker Robert D. , Rhodes Bobbie , Fedorka-Cray Paula J. , Simjee Shabbir , Zhao Shaohua 
Published: October 2006

ABSTRACT

Molecular characterization (e.g., DNA-based typing methods) of
Salmonella
isolates is frequently employed to compare and distinguish clinical isolates recovered from animals and from patients with food-borne disease and nosocomial infections. In this study, we compared the abilities of different phenotyping and genotyping methods to distinguish isolates of
Salmonella enterica
serovar Typhimurium from different food animal sources. One hundred twenty-eight
S. enterica
serovar Typhimurium strains isolated from cattle, pigs, chickens, and turkeys or derived food products were characterized using pulsed-field gel electrophoresis (PFGE), repetitive element PCR (Rep-PCR), multilocus sequence typing (MLST), plasmid profiling, and antimicrobial susceptibility testing. Among the 128
Salmonella
isolates tested, we observed 84 Rep-PCR profiles, 86 PFGE patterns, 89 MLST patterns, 36 plasmid profiles, and 38 susceptibility profiles. The molecular typing methods, i.e., PFGE, MLST, and Rep-PCR, demonstrated the best discriminatory power among
Salmonella
isolates. However, no apparent correlation was evident between the results of one molecular typing method and those of the others, suggesting that a combination of multiple methods is needed to differentiate
S. enterica
serovar Typhimurium isolates that genetically cluster according to one particular typing method.
Use of a Single-Nucleotide Polymorphism Genotyping System To Demonstrate the Unique Epidemiology of Methicillin-Resistant
Staphylococcus aureus
in Remote Aboriginal Communities
Authors: McDonald Malcolm , Dougall Annette , Holt Deborah , Huygens Flavia , Oppedisano Frances , Giffard Philip M. , Inman-Bamber John , Stephens Alex J. , Towers Rebecca , Carapetis Jonathan R. , Currie Bart J. 
Published: October 2006

ABSTRACT

Community-acquired methicillin-resistant
Staphylococcus aureus
(CA-MRSA) has emerged as a major public health problem in Australia, as in many other parts of the world. High rates of CA-MRSA skin and soft tissue infection have been reported from Aboriginal communities. We used a single-nucleotide polymorphism (SNP) genotyping typing system based on the multilocus sequence type (MLST) database to investigate the epidemiology of CA-MRSA and methicillin-sensitive
S. aureus
(MSSA) over a 12-month period in three remote Aboriginal communities of Northern Australia. This was supplemented by real-time PCR for Panton-Valentine leukocidin (PVL) genes, staphylococcal cassette chromosome
mec
(SCC
mec
) typing, and antimicrobial susceptibility testing.
S. aureus
was recovered from pyoderma lesions on 221 occasions and throat swabs on 44 occasions. The median monthly recovery rate of
S. aureus
from skin sores was 58% (interquartile range, 62 to 78%), and there was no seasonal variation. Twenty-three percent of isolates were CA-MRSA; the proportion was similar across the communities and did not vary over the study period. Erythromycin resistance was found in 47% of CA-MRSA and 21% of MSSA. SNP-based typing identified 14 different clonal complexes (cc); however, cc75 was predominant, accounting for 71% of CA-MRSA isolates. These were confirmed as ST75-like by using an additional SNP and MLST of selected isolates. All but one of the cc75 isolates had SSC
mec
type IV (one had type V), and all were PVL negative. Monthly tracking of SNP-based cc types showed a highly dynamic process. ST75-MRSA-IV appears to be unique to the region and probably evolved de novo in remote Aboriginal communities.
Molecular Identification of Black-Grain Mycetoma Agents
Authors: Desnos-Ollivier Marie , Bretagne Stéphane , Dromer Françoise , Lortholary Olivier , Dannaoui Eric 
Published: October 2006

ABSTRACTBlack-grain mycetomas are subcutaneous devastating chronic infections due to several dematiaceous fungi. They are diagnosed mostly in tropical countries. Identification of these fungi with standard mycological procedures is difficult because of their poor or delayed sporulation. The aim of this study was thus to assess the accuracy of molecular identification of these fungi. A total of 54 strains, mostly of clinical origin, were used, including 15Madurella mycetomatis, 6Madurella grisea, 12Leptosphaeria senegalensis, 4Leptosphaeria tompkinsii, 6Pyrenochaetaspp., 4Curvularia lunata, and 7Exophiala jeanselmeistrains. The internal transcribed spacer 1 (ITS1)-5.8S-ITS2 DNA region was amplified by using universal fungal primers and sequenced. Both intra- and interspecies sequence similarities were assessed.Madurella mycetomatisappeared to be a homogeneous species. More intraspecies variations were found forC. lunataandE. jeanselmei, leading, in some instances, to changes in the initial identification.L. senegalensisandL. tompkinsiishowed intraspecies similarities of >99%, but similarity between the two species was <88%. Intergenera and interspecies variations were important, with sequence homologies of <81% between genera. In contrast,Pyrenochaeta romeroiandM. griseaappeared to be heterogeneous, with intraspecies similarities of 40 to 100% and 53 to 100%, respectively, which suggest either erroneous identification or the need for taxonomic revision. Epidemiological and therapeutic studies could benefit from a precise identification of the fungi responsible for black-grain mycetoma based not only on phenotypical characteristics but also on ITS sequencing.
Candida guilliermondii
, an Opportunistic Fungal Pathogen with Decreased Susceptibility to Fluconazole: Geographic and Temporal Trends from the ARTEMIS DISK Antifungal Surveillance Program
Authors: Pfaller M. A. , Diekema D. J. , Mendez M. , Kibbler C. , Erzsebet P. , Chang S.-C. , Gibbs D. L. , Newell V. A. ,   the Global Antifungal Surveillance Group
Published: October 2006

ABSTRACT

Although a rare cause of invasive candidiasis,
Candida guilliermondii
has been reported to exhibit decreased susceptibility to antifungal agents. Aside from case reports and small surveys, there is little information regarding the epidemiology and antifungal susceptibility profile of
C. guilliermondii
. We report geographic and temporal trends in the isolation and antifungal susceptibilities of 1,029
C. guilliermondii
clinical isolates collected from 127 medical centers as part of the ARTEMIS DISK Antifungal Surveillance Program. In addition, we report the in vitro susceptibility of 132 bloodstream isolates of
C. guilliermondii
to caspofungin.
C. guilliermondii
represented 1.4% of the 75,761 isolates collected from 2001 to 2003 and was most common among isolates from Latin America (3.7% versus 0.6 to 1.1%). Decreased susceptibility to fluconazole was noted (75% susceptible; range, 68 to 77% across regions), and voriconazole was more active in vitro against
C. guilliermondii
than fluconazole (91% susceptible; range, 88 to 93% across regions). Fluconazole was least active against isolates from dermatology (58%) and surgical (69%) services and against isolates associated with skin and soft tissue infection (68%, compared to 85% susceptible for bloodstream isolates). There was no evidence of increasing azole resistance over time among
C. guilliermondii
isolates tested from 2001 to 2003. Of 132 bloodstream isolates of
C. guilliermondii
tested against caspofungin, most were inhibited by ≤2 μg/ml (96%; MIC
50
/MIC
90
, 0.5/1.0 μg/ml).
C. guilliermondii
, a species that exhibits reduced susceptibility to fluconazole, is the sixth most frequently isolated
Candida
species from this large survey and may be an emerging pathogen in Latin America.
Multiplex Real-Time PCR Assay for Simultaneous Detection of
Acanthamoeba
spp.,
Balamuthia mandrillaris
, and
Naegleria fowleri
Authors: Qvarnstrom Yvonne , Visvesvara Govinda S. , Sriram Rama , da Silva Alexandre J. 
Published: October 2006

ABSTRACT

Infections caused by
Naegleria fowleri
,
Acanthamoeba
spp., and
Balamuthia mandrillaris
occur throughout the world and pose many diagnostic challenges. To date, at least 440 cases of severe central nervous system infections caused by these amebas have been documented worldwide. Rapid and specific identification of these free-living amebas in clinical samples is of crucial importance for efficient case management. We have developed a triplex real-time TaqMan PCR assay that can simultaneously identify
Acanthamoeba
spp.,
B. mandrillaris
, and
N. fowleri
in the same PCR vessel. The assay was validated with 22 well-characterized amebic strains harvested from cultures and nine clinical specimens that were previously characterized by in vitro culture and/or immunofluorescence assay. The triplex assay demonstrated high specificity and a rapid test completion time of less than 5 h from the reception of the specimen in the laboratory. This assay was able to detect one single ameba per sample analyzed, as determined with cerebrospinal fluid spiked with diluted cultured amebas. This assay could become useful for fast laboratory diagnostic assessment of amebic infections (caused by free-living amebas) in laboratories with adequate infrastructure to perform real-time PCR testing.
Evaluation of the BD Phoenix Automated Microbiology System for Identification and Antimicrobial Susceptibility Testing of
Enterobacteriaceae
Authors: Carroll Karen C. , Glanz Brian D. , Borek Anita P. , Burger Chad , Bhally Hasan S. , Henciak Susan , Flayhart Diane 
Published: October 2006

ABSTRACT

We evaluated the accuracy of the BD Phoenix system for the identification (ID) and antimicrobial susceptibility testing (AST) of 251 isolates of the family
Enterobacteriaceae
representing 31 species. Organisms were inoculated onto the Phoenix panel according to the manufacturer's instructions. The results from conventional biochemical tests were used for the reference method for ID. Agar dilution, performed according to the CLSI guidelines, was the reference AST method. Essential and categorical agreements were determined. The overall levels of agreement for the genus- and species-level identifications were 95.6% and 94.4%, respectively. Fourteen isolates were incorrectly identified by the Phoenix system; 10 of these were incorrectly identified to the species level. Three of these were
Enterobacter
(
Pantoea
) species and four of these were
Shigella
spp. misidentified as
Escherichia coli
. For AST results, the essential and categorical agreements were 98.7% and 97.9%, respectively. The very major error, major error, and minor error rates were 0.38%, 0.33%, and 1.8%, respectively. Six isolates (three
E. coli
isolates and three
Klebsiella
isolates) were extended-spectrum β-lactamase producers. All six were flagged by the Phoenix system expert rules. The Phoenix system compares favorably to traditional methods for ID and AST of
Enterobacteriaceae
.
Molecular Epidemiology of Rotavirus Diarrhea among Children and Adults in Nepal: Detection of G12 Strains with P[6] or P[8] and a G11P[25] Strain
Authors: Uchida Ryuichi , Pandey Basu Dev , Sherchand Jeevan Bahadur , Ahmed Kamurddin , Yokoo Michiyo , Nakagomi Toyoko , Cuevas Luis E. , Cunliffe Nigel A. , Hart C. A. , Nakagomi Osamu 
Published: October 2006

ABSTRACT
In anticipation of a rotavirus vaccine in Nepal, this study was undertaken to determine the distribution of the G and P serotypes and electropherotypes of rotaviruses in order to examine if there is any emerging serotype or unusual strain circulating in children and adults in Nepal. Of 1,315 diarrheal stool specimens, rotavirus was detected by an enzyme-linked immunosorbent assay in 116 (17%) of 666 patients less than 5 years of age, in 18 (7%) of 260 patients 5 to 14 years of age, and in 19 (5%) of 358 patients 15 years of age and older. Approximately 75% of rotavirus diarrhea occurred in children less than 5 years of age. Approximately 70% of rotaviruses found in each of the three age groups belonged to serotype G1P[8]. Interestingly, there were 29 (20%) G12 rotaviruses carrying either P[8] or P[6] and one (0.7%) G11 rotavirus carrying an unusual P[25] genotype. RNA polyacrylamide gel electrophoresis discriminated 19 strains (electropherotypes), among which there were three codominant strains carrying G1P[8] and long RNA patterns. Five electropherotypes were discriminated among G12 rotaviruses, all of which had long RNA patterns. The fact that 20% of rotaviruses were G12 strains carrying either P[8] or P[6] and had multiple electropherotypes suggest that G12 strains are not more rare strains but that they pose an emerging challenge to current and future vaccines. The presence of multiple strains as defined by electropherotypes suggests the richness of the rotavirus gene pool in Nepal, where unusual strains may continue to emerge.
Comparative Evaluation of Three Commercially Available Methodologies for Hepatitis C Virus Genotyping
Authors: Schutzbank Ted E. , Sefers Susan E. , Kahmann Nicole , Li Haijing , Tang Yi-Wei 
Published: October 2006

ABSTRACTWe compared the performances of three hepatitis C virus genotyping methodologies supplied by Bayer, Abbott, and Third Wave Technologies. Genotypes were determined for 136 of 137 specimens by the Bayer method, 121 of 137 specimens by the Invader assay, and only 77 of 137 specimens by the Abbott assay. All reported genotypes were concordant by all three methods.
Comparison of Three Commercial Assays and a Modified Disk Diffusion Assay with Two Broth Microdilution Reference Assays for Testing Zygomycetes,
Aspergillus
spp.,
Candida
spp., and
Cryptococcus neoformans
with Posaconazole and Amphotericin B
Authors: Espinel-Ingroff A. 
Published: October 2006

ABSTRACT

We compared posaconazole M27-A2 and M38-A MICs to Etest and YeastOne MICs for 92 zygomycetes, 126
Aspergillus
isolates, 110
Candida
isolates, and
Cryptococcus neoformans
. Reference MICs were also correlated with inhibition zone diameters in millimeters (modified M44-A disk and Neo-Sensitabs tablet methods). Etest MICs were obtained on solidified (1.5% agar) RPMI 1640 (2% dextrose), and zone diameters were obtained on supplemented (2% glucose and 0.5 μg/ml methylene blue [for all isolates]) and nonsupplemented Mueller-Hinton (MH; molds only) agar. MICs and zone diameters were obtained between 16 and 72 h. The overall agreement (% MIC pairs within a three-dilution range) between reference posaconazole and YeastOne MICs was 98 to 100% at 16 to 24 h for zygomycetes and yeasts and 99% at 24 to 48 h for
Aspergillus
. The overall agreement was lower between reference posaconazole and Etest MICs (94 to 97%) and by both methods with amphotericin B for all species (95 to 99.3%). For yeasts, the correlation coefficient was similar between reference posaconazole MICs and either disk (
R
, 0.810) or tablet (
R
, 0.769) zone diameter at 24 h and was superior on MH agar for molds at 16 to 48 h (
R
, 0.804 and 0.799 for disk and tablet, respectively). For amphotericin B, the best correlation between reference MICs and zone diameters was observed at 16 to 48 h for molds on MH agar (
R
, 0.736 to 0.812 and 0.765 to 0.749 for disk and tablet, respectively) and at 48 h for yeasts (
R
, 0.681 and 0.503 for disk and tablet, respectively). These data suggest the potential value of these alternative broth dilution and agar diffusion methods for testing posaconazole and amphotericin B in the clinical laboratory against the species evaluated.