bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation in Resistance of
Mycobacterium paratuberculosis
to Acid Environments as a Function of Culture Medium
Authors: Sung Nackmoon , Collins Michael T. 
Published: November 2003

ABSTRACT

Acid resistance of
Mycobacterium paratuberculosis
was examined as a function of growth conditions (i.e., in vitro growth medium and pH).
M. paratuberculosis
was cultured in either fatty acid-containing medium (7H9-OADC) or glycerol-containing medium (WR-GD or 7H9-GD) at two culture pHs (pHs 6.0 and 6.8). Organisms produced in these six medium and pH conditions were then tested for resistance to acetate buffer at pHs 3, 4, 5, and 6 at 20°C. A radiometric culture method (BACTEC) was used to quantify viable
M. paratuberculosis
cell data at various acid exposure times, and
D
values (decimal reduction times, or the times required to kill a 1-log
10
concentration of bacteria) were determined. Soluble proteins of
M. paratuberculosis
grown under all six conditions were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to identify proteins that may be associated with acid resistance or susceptibility. The culture medium affected growth rate and morphology: thin floating sheets of cells were observed in 7H9-OADC versus confluent, thick, waxy, and wrinkled pellicles in WR-GD. Culture medium pH affected growth rate (which was highest at pH 6.0), but it had little or no effect on
D
values for
M. paratuberculosis
at any test pH. When grown in 7H9-OADC,
M. paratuberculosis
was more acid resistant at all test pHs (higher
D
values) than when grown in WR-GD. Glycerol appeared to be the culture medium component most responsible for lower levels of
M. paratuberculosis
acid resistance. When glycerol was substituted for OADC in the 7H9 medium,
D
values were significantly lower than those of 7H9-OADC-grown
M. paratuberculosis
and were approximately the same as those for
M. paratuberculosis
grown in WR-GD medium. Comparison of the SDS-PAGE protein profiles for
M. paratuberculosis
cultures grown in 7H9-OADC, WR-GD, or 7H9-GD medium revealed that increased expression of 34.2- and 14.0-kDa proteins was associated with higher levels of acid resistance of
M. paratuberculosis
grown in 7H9-OADC medium and that 56.6- and 41.3-kDa proteins were associated with lower levels of acid resistance. This is the first report showing that in vitro culture conditions significantly affect growth characteristics, acid resistance, and protein expression of
M. paratuberculosis
, and the results emphasize the importance of culture conditions for in vitro susceptibility studies.
The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function
Authors: Adamczyk Justyna , Hesselsoe Martin , Iversen Niels , Horn Matthias , Lehner Angelika , Nielsen Per Halkjaer , Schloter Michael , Roslev Peter , Wagner Michael 
Published: November 2003

ABSTRACT

A new microarray method, the isotope array approach, for identifying microorganisms which consume a
14
C-labeled substrate within complex microbial communities was developed. Experiments were performed with a small microarray consisting of oligonucleotide probes targeting the 16S rRNA of ammonia-oxidizing bacteria (AOB). Total RNA was extracted from a pure culture of
Nitrosomonas eutropha
grown in the presence of [
14
C]bicarbonate. After fluorescence labeling of the RNA and microarray hybridization, scanning of all probe spots for fluorescence and radioactivity revealed that specific signals were obtained and that the incorporation of
14
C into rRNA could be detected unambiguously. Subsequently, we were able to demonstrate the suitability of the isotope array approach for monitoring community composition and CO
2
fixation activity of AOB in two nitrifying activated-sludge samples which were incubated with [
14
C]bicarbonate for up to 26 h. AOB community structure in the activated-sludge samples, as predicted by the microarray hybridization pattern, was confirmed by quantitative fluorescence in situ hybridization (FISH) and comparative
amoA
sequence analyses. CO
2
fixation activities of the AOB populations within the complex activated-sludge communities were detectable on the microarray by
14
C incorporation and were confirmed independently by combining FISH and microautoradiography. AOB rRNA from activated sludge incubated with radioactive bicarbonate in the presence of allylthiourea as an inhibitor of AOB activity showed no incorporation of
14
C and thus was not detectable on the radioactivity scans of the microarray. These results suggest that the isotope array can be used in a PCR-independent manner to exploit the high parallelism and discriminatory power of microarrays for the direct identification of microorganisms which consume a specific substrate in the environment.
Sequencing and Characterization of pBM400 from
Bacillus megaterium
QM B1551
Authors: Scholle Michael D. , White Christen A. , Kunnimalaiyaan Muthusamy , Vary Patricia S. 
Published: November 2003

ABSTRACT

Bacillus
megaterium
QM B1551 plasmid pBM400, one of seven indigenous
plasmids, has been labeled with a selectable marker, isolated,
completely sequenced, and partially characterized. A sequence of 53,903
bp was generated, revealing a total of 50 predicted open reading frames
(ORFs); 33 were carried on one strand and 17 were carried on the other.
These ORFs comprised 57% of the pBM400 sequence. Besides the
replicon region and a complete rRNA operon that have previously been
described, several interesting genes were found, including genes for
predicted proteins for cell division (FtsZ and FtsK), DNA-RNA
interaction (FtsK, Int/Rec, and reverse transcriptase), germination
(CwlJ), styrene degradation (StyA), and heavy metal resistance (Cu-Cd
export and ATPase). Three of the ORF products had high similarities to
proteins from the
Bacillus anthracis
virulence plasmid pXO1.
An insertion element with similarity to the IS
256
family and
several hypothetical proteins similar to those from the chromosomes of
other
Bacillus
and
Lactococcus
species were present.
This study provides a basis for isolation and sequencing of other
high-molecular-weight plasmids from QM B1551 and for understanding the
role of megaplasmids in gram-positive bacteria. The genes carried by
pBM400 suggest a possible role of this plasmid in the survival of
B. megaterium
in hostile environments with heavy metals or
styrene and also suggest that there has been an exchange of genes
within the gram-positive bacteria, including
pathogens.
Growth of
Vibrio cholerae
O1 in Red Tide Waters off California
Authors: Mouriño-Pérez Rosa R. , Worden Alexandra Z. , Azam Farooq 
Published: November 2003

ABSTRACT

Vibrio cholerae
serotype O1 is autochthonous to estuarine and coastal waters. However, its population dynamics in such environments are not well understood. We tested the proliferation of
V. cholerae
N16961 during a
Lingulodinium polyedrum
bloom, as well as other seawater conditions. Microcosms containing 100-kDa-filtered seawater were inoculated with
V. cholerae
or the 0.6-μm-pore-size filterable fraction of seawater assemblages. These cultures were diluted 10-fold with fresh 100-kDa-filtered seawater every 48 h for four cycles. Growth rates ranged from 0.3 to 14.3 day
−1
(4.2 day
−1
± 3.9) for
V. cholerae
and 0.1 to 9.7 day
−1
(2.2 ± 2.8 day
−1
) for bacterial assemblage. Our results suggest that dissolved organic matter during intense phytoplankton blooms has the potential to support explosive growth of
V. cholerae
in seawater. Under the conditions tested, free-living
V. cholerae
was able to reach concentrations per milliliter that were up to 3 orders of magnitude higher than the known minimum infectious dose (10
4
cell ml
−1
) and remained viable under many conditions. If applicable to the complex conditions in marine ecosystems, our results suggest an important role of the growth of free-living
V. cholerae
in disease propagation and prevention during phytoplankton blooms.
Development of a Synthetic Minimal Medium for
Listeria monocytogenes
Authors: Tsai Hsiang-Ning , Hodgson David A. 
Published: November 2003

ABSTRACT

A defined solid and liquid minimal medium, HTM, which contained methionine and cysteine as the sole amino acids, was developed for
Listeria monocytogenes
. Complex broth-grown
L. monocytogenes
had to adapt to HTM by inducing amino acid biosyntheis. HTM is the simplest minimal medium available for growth of
L. monocytogenes
.
Mycobacterium xenopi
and Drinking Water Biofilms
Authors: Dailloux M. , Albert M. , Laurain C. , Andolfatto S. , Lozniewski A. , Hartemann P. , Mathieu L. 
Published: November 2003

ABSTRACT

The ability of
Mycobacterium xenopi
to colonize an experimental drinking water distribution system (a Propella reactor) was investigated.
M. xenopi
was present in the biofilm within an hour following its introduction. After 9 weeks, it was always present in the outlet water (1 to 10 CFU 100 ml
−1
) and inside the biofilm (10
2
to 10
3
CFU cm
−2
). Biofilms may be considered reservoirs for the survival of
M. xenopi
.
Association of Genomic O Island 122 of
Escherichia coli
EDL 933 with Verocytotoxin-Producing
Escherichia coli
Seropathotypes That Are Linked to Epidemic and/or Serious Disease
Authors: Karmali Mohamed A. , Mascarenhas Mariola , Shen Songhai , Ziebell Kim , Johnson Shelley , Reid-Smith Richard , Isaac-Renton Judith , Clark Clifford , Rahn Kris , Kaper James B. 
Published: November 2003

ABSTRACT

The distribution of EDL 933 O island 122 (OI-122) was investigated in 70 strains of Verocytotoxin-producing
Escherichia coli
(VTEC) of multiple serotypes that were classified into five “seropathotypes” (A through E) based on the reported occurrence of serotypes in human disease, in outbreaks, and/or in the hemolytic-uremic syndrome (HUS). Seropathotype A comprised 10 serotype O157:H7 and 3 serotype O157:NM strains. Seropathotype B (associated with outbreaks and HUS but less commonly than serotype O157:H7) comprised three strains each of serotypes O26:H11, O103:H2, O111:NM, O121:H19, and O145:NM. Seropathotype C comprised four strains each of serotypes O91:H21 and O113:H21 and eight strains of other serotypes that have been associated with sporadic HUS but not typically with outbreaks. Seropathotype D comprised 14 strains of serotypes that have been associated with diarrhea but not with outbreaks or HUS, and seropathotype E comprised animal VTEC strains of serotypes not implicated in human disease. All strains were tested for four EDL 933 OI-122 virulence genes (Z4321, Z4326, Z4332, and Z4333) by PCR. Negative PCRs were confirmed by Southern hybridization. Overall, 28 (40%) strains contained OI-122 (positive for all four virulence genes), 27 (38.6%) contained an “incomplete” OI-122 (positive for one to three genes), and 15 (21.4%) strains did not contain OI-122. The seropathotype distribution of complete OI-122 was as follows: 100% for seropathotype A, 60% for B, 36% for C, 15% for D, and 0% for E. The differences in the frequency of OI-122 between seropathotypes A, B, and C (associated with HUS) and seropathotypes D and E (not associated with HUS) and between seropathotypes A and B (associated with epidemic disease) and seropathotypes C, D, and E (not associated with epidemic disease) were highly significant (
P
< 0.0001).
C
6
Test as an Indicator of Therapy Outcome for Patients with Localized or Disseminated Lyme Borreliosis
Authors: Philipp Mario T. , Marques Adriana R. , Fawcett Paul T. , Dally Leonard G. , Martin Dale S. 
Published: November 2003

ABSTRACT

Management of Lyme disease would benefit from a test to assess therapy outcome. Such a test could be employed to ascertain if treatment of early Lyme disease was successful and would be helpful to clinicians assessing patients with lingering posttreatment symptoms. We reported recently that levels of the antibody to C
6
, a
Borrelia burgdorferi-
derived peptide that is used as an antigen in the C
6
-Lyme diagnostic test, declined after successful antibiotic treatment of Lyme borreliosis patients. We assessed retrospectively the change in anti-C
6
antibody titers in 131 patients with either early localized disease (erythema migrans) or disseminated disease. All of these patients were treated with antibiotics and were free of the clinical signs shown at presentation within 12 weeks after the initiation of treatment. Decreases in reciprocal geometric mean titers (rGMT) of the anti-C
6
antibody were quantified for the subpopulation of 45 patients whose baseline rGMT were ≥80 and whose second serum specimens were obtained at least 6 months after the baseline specimen. Eighty percent of this patient group (36 of 45) experienced a ≥4-fold decrease in their rGMT (
P
< 0.0003). These results suggest that a change in the anti-C
6
antibody titer may serve as an indicator of therapy outcome for patients with localized or disseminated Lyme borreliosis.
Study of Animal-Borne Infections in the Mucosas of Patients with Inflammatory Bowel Disease and Population-Based Controls
Authors: Bernstein Charles N. , Nayar Gopi , Hamel Andre , Blanchard James F. 
Published: November 2003

ABSTRACT

Crohn's disease may be triggered by an infection, and it is plausible to consider that such an infection may be animal borne and ingested with our food. There has been considerable interest in the past in determining whether
Mycobacterium avium
subsp.
paratuberculosis
(
M. avium
) might be the etiologic agent in Crohn's disease since it causes a disease in cattle that is similar to Crohn's disease in humans. We aimed to determine if there was an association between Crohn's disease and infection with
M. avium
or other zoonotic agents and compared the findings with those for patients with ulcerative colitis, unaffected siblings of Crohn's disease patients, or population-based controls without inflammatory bowel disease. Patients under age 50 years with Crohn's disease or ulcerative colitis, unaffected siblings of patients, or healthy controls drawn from a population-based age- and gender-matched registry were enrolled in a study in which subjects submitted to a questionnaire survey and venipuncture. A nested cohort underwent colonoscopy plus biopsy. Samples were batched and submitted to PCR for the detection of
M. avium
and other zoonotic agents known to cause predominately intestinal disease in cattle, sheep, or swine. Only one patient with ulcerative colitis, no patients with Crohn's disease, and none of the sibling controls were positive for
M. avium
, whereas 6 of 19 healthy controls were positive for
M. avium
. Since the control subjects were significantly older than the case patients, we studied another 11 patients with inflammatory bowel disease who were older than age 50 years, and another single subject with ulcerative colitis was positive for
M. avium
. One other subject older than age 50 years with ulcerative colitis was positive for circovirus, a swine-borne agent of infection. In conclusion, by performing PCR with mucosal samples from patients with Crohn's disease and controls, no association between Crohn's disease and infection with
M. avium
or any of the other six zoonotic agents studied could be found.
Evaluation of the Polymorphisms Associated with Tandem Repeats for
Pseudomonas aeruginosa
Strain Typing
Authors: Onteniente Lucie , Brisse Sylvain , Tassios Panayotis T. , Vergnaud Gilles 
Published: November 2003

ABSTRACT

We report on the development of a scheme for the typing of
Pseudomonas aeruginosa
, multiple-locus variable number of tandem repeat (VNTR) analysis (MLVA). We first evaluated the polymorphisms of 201 tandem repeat loci selected from more than 3,000 such sequences present in strain PAO1 with a test collection of 12 genotypically distinct clinical strains. Seven VNTR loci which can be easily scored with the technology used here were identified and used to genotype a collection of 89 clinical isolates that had previously been classified into 46 ribotypes, including 2 widespread ribotypes. Seventy-one different MLVA genotypes could be distinguished. With only two exceptions, strains with identical ribotypes were grouped together upon cluster analysis of the MLVA data. The 27 isolates with the most frequent ribotype were divided into 14 MLVA types, and the 18 isolates with the second most frequent ribotype were divided into 15 MLVA types. Analysis of a subset of 17 strains belonging to the major ribotype by pulsed-field gel electrophoresis with the enzyme
Spe
I distinguished seven types, identical to the number of MLVA types in this subset. Our data show that MLVA typing of
P. aeruginosa
based on the first set of loci has a high discriminatory power. Because MLVA is highly reproducible and easily portable among laboratories, it represents a very promising tool for the molecular surveillance of
P. aeruginosa
. A free, online strain identification service based on the genotyping data produced herein has been developed.
Comparison of the NucliSens Basic Kit (Nucleic Acid Sequence-Based Amplification) and the Argene Biosoft Enterovirus Consensus Reverse Transcription-PCR Assays for Rapid Detection of Enterovirus RNA in Clinical Specimens
Authors: Landry Marie L. , Garner Robin , Ferguson David 
Published: November 2003

ABSTRACT
Samples were tested for enterovirus by nucleic acid sequence-based amplification (NASBA) (NucliSens Basic kit; BioMerieux), reverse transcription-PCR (RT-PCR) (Enterovirus Consensus RT-PCR kit; Argene Biosoft), and virus isolation. Eighty-two samples were tested, and 44 were positive, 34 by both NASBA and RT-PCR and 5 each by NASBA or RT-PCR only. Two nasopharyngeal samples positive only by RT-PCR were determined to be rhinovirus. Of 42 enterovirus-positive samples, NASBA detected 39 (92.9%) and RT-PCR detected 37 (88.1%). The NucliSens Basic kit and the Argene Biosoft RT-PCR had comparable sensitivities for detection of enterovirus RNA, and both molecular methods were more sensitive than culture, which detected only 60.5% of positive samples. NASBA could be completed in 6.5 h versus 9 h for the Argene Biosoft RT-PCR kit.
Pulsed-Field Gel Electrophoresis Typing of Oxacillin-ResistantStaphylococcus aureusIsolates from the United States: Establishing a National Database
Authors: McDougal Linda K. , Steward Christine D. , Killgore George E. , Chaitram Jasmine M. , McAllister Sigrid K. , Tenover Fred C. 
Published: November 2003

ABSTRACTOxacillin-resistantStaphylococcus aureus(ORSA) is a virulent pathogen responsible for both health care-associated and community onset disease. We usedSmaI-digested genomic DNA separated by pulsed-field gel electrophoresis (PFGE) to characterize 957S. aureusisolates and establish a database of PFGE patterns. In addition to PFGE patterns of U.S. strains, the database contains patterns of representative epidemic-type strains from the United Kingdom, Canada, and Australia; previously described ORSA clonal-type isolates; 13 vancomycin-intermediateS. aureus(VISA) isolates, and two high-level vancomycin-resistant,vanA-positive strains (VRSA). Among the isolates from the United States, we identified eight lineages, designated as pulsed-field types (PFTs) USA100 through USA800, seven of which included both ORSA and oxacillin-susceptibleS. aureusisolates. With the exception of the PFT pairs USA100 and USA800, and USA300 and USA500, each of the PFTs had a unique multilocus sequence type andspatype motif. The USA100 PFT, previously designated as the New York/Tokyo clone, was the most common PFT in the database, representing 44% of the ORSA isolates. USA100 isolates were typically multiresistant and included all but one of the U.S. VISA strains and both VRSA isolates. Multiresistant ORSA isolates from the USA200, -500, and -600 PFTs have PFGE patterns similar to those of previously described epidemic strains from Europe and Australia. The USA300 and -400 PFTs contained community isolates resistant only to β-lactam drugs and erythromycin. Noticeably absent from the U.S. database were isolates with the previously described Brazilian and EMRSA15 PFGE patterns. These data suggest that there are a limited number of ORSA genotypes present in the United States.
Microarrays for Genotyping Human Group A Rotavirus by Multiplex Capture and Type-Specific Primer Extension
Authors: Lovmar Lovisa , Fock Caroline , Espinoza Felix , Bucardo Filemon , Syvänen Ann-Christine , Bondeson Kåre 
Published: November 2003

ABSTRACT
Human group A rotavirus (HRV) is the major cause of severe gastroenteritis in infants worldwide. HRV shares the feature of a high degree of genetic diversity with many other RNA viruses, and therefore, genotyping of this organism is more complicated than genotyping of more stable DNA viruses. We describe a novel microarray-based method that allows high-throughput genotyping of RNA viruses with a high degree of polymorphism by multiplex capture and type-specific extension on microarrays. Denatured reverse transcription (RT)-PCR products derived from two outer capsid genes of clinical isolates of HRV were hybridized to immobilized capture oligonucleotides representing the most commonly occurring P and G genotypes on a microarray. Specific primer extension of the type-specific capture oligonucleotides was applied to incorporate the fluorescent nucleotide analogue cyanine 5-labeled dUTP as a detectable label. Laser scanning and fluorescence detection of the microarrays was followed by visual or computer-assisted interpretation of the fluorescence patterns generated on the microarrays. Initially, the method detected HRV in all 40 samples and correctly determined both the G and the P genotypes of 35 of the 40 strains analyzed. After modification by inclusion of additional capture oligonucleotides specific for the initially unassigned genotypes, all genotypes could be correctly defined. The results of genotyping with the microarray fully agreed with the results obtained by nucleotide sequence analysis and sequence-specific multiplex RT-PCR. Owing to its robustness, simplicity, and general utility, the microarray-based method may gain wide applicability for the genotyping of microorganisms, including highly variable RNA and DNA viruses.
Rapid Colorimetric Method for Testing Susceptibility of
Mycobacterium tuberculosis
to Isoniazid and Rifampin in Liquid Cultures
Authors: Syre H. , Phyu S. , Sandven P. , Bjorvatn B. , Grewal H. M. S. 
Published: November 2003

ABSTRACT

We have developed a rapid colorimetric method for testing the susceptibility of
M. tuberculosis
to isoniazid (INH) and rifampin (RIF) based on incorporation of nitrate in broth cultures containing growth supplements. The performance of this colorimetric nitrate reductase-based antibiotic susceptibility (CONRAS) test was compared with that of the radiometric BACTEC 460TB system in determining the susceptibilities of 74
M. tuberculosis
strains to INH and RIF. By using the BACTEC 460TB system as the “gold standard,” the sensitivity (i.e., the ability to detect true drug resistance) and specificity (i.e., the ability to detect true drug susceptibility) of the CONRAS test were 100 and 95% for INH and 94 and 100% for RIF, respectively. The repeatability of the CONRAS test was excellent (for INH, kappa = 1 and
P
< 0.001; for RIF, kappa = 0.88 and
P
< 0.001). For the majority of strains, results were obtained within 5 days. The CONRAS test is rapid, accurate, and inexpensive and is an adequate alternative, particularly for resource-poor countries.
agr
-Dependent Bacterial Interference Has No Impact on Long-Term Colonization of
Staphylococcus aureus
during Persistent Airway Infection of Cystic Fibrosis Patients
Authors: Kahl Barbara C. , Becker Karsten , Friedrich Alexander W. , Clasen Julia , Sinha Bhanu , von Eiff Christof , Peters Georg 
Published: November 2003

ABSTRACT

The
agr
specificity group distribution of persistent
Staphylococcus aureus
clones recovered from the airways of cystic fibrosis (CF) patients did not differ from that of isolates recovered from various clinical infections and healthy nasal carriers. The success of CF clones in terms of cocolonization and/or infection with
S. aureus
, prevalence of clones, or persistence appeared to be independent of
agr
group specificity.