Achieving 100% typeability of Pseudomonas aeruginosa by pulsed-field gel electrophoresis.
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Bacterial Typing Techniques↗
Biomedical subjects
B Tümmler
Publications and source records attributed to B Tümmler.
Distinguishing species of the Burkholderia cepacia complex and Burkholderia gladioli by automated ribotyping.
Several species belonging to the genus Burkholderia are clinically relevant, opportunistic pathogens that inhabit major environmental reservoirs. Consequently, the availability of means for adequate identification and epidemiological characterization of individual environmental or clinical isolates is mandatory. In the present communication we describe the use of the Riboprinter microbial characterization system (Qualicon, Warwick, United Kingdom) for automated ribotyping of 104 strains of Burkholderia species from diverse sources, including several publicly accessible collections. The main outcome of this analysis was that all strains were typeable and that strains of Burkholderia gladioli and of each species of the B. cepacia complex, including B. multivorans, B. stabilis, and B. vietnamiensis, were effectively discriminated. Furthermore, different ribotypes were discerned within each species. Ribotyping results were in general agreement with strain classification based on restriction fragment analysis of 16S ribosomal amplicons, but the resolution of ribotyping was much higher. This enabled automated molecular typing below the species level. Cluster analysis of the patterns obtained by ribotyping (riboprints) showed that within B. gladioli, B. multivorans, and B. cepacia genomovar VI, the different riboprints identified always clustered together. Riboprints of B. cepacia genomovars I and III, B. stabilis, and B. vietnamiensis did not show distinct clustering but rather exhibited the formation of loose assemblages within which several smaller, genomovar-specific clusters were delineated. Therefore, ribotyping proved useful for genomovar identification. Analysis of serial isolates from individual patients demonstrated that infection with a single ribotype had occurred, despite minor genetic differences that were detected by pulsed-field gel electrophoresis of DNA macrorestriction fragments. The automated approach allows very rapid and reliable identification and epidemiological characterization of strains and generates an easily manageable database suited for expansion with information on additional bacterial isolates.
Automation↗
Applicability of different antibodies for immunohistochemical localization of CFTR in sweat glands from healthy controls and from patients with cystic fibrosis.
The hereditary disease cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Understanding of the consequences of CFTR gene mutations is derived chiefly from in vitro studies on heterologous cell cultures and on cells hyperexpressing CFTR. Data from ex vivo studies on human tissue are scarce and contradictory, a fact which is in part explained by secondary tissue destruction in most affected organs. The purpose of this study was to establish conditions under which wild-type and mutated CFTR can be studied in affected human tissue. Sweat glands carry the basic defect underlying CF and are not affected by tissue destruction and inflammation. Therefore, we used this tissue to test a panel of eight different CFTR antibodies under various fixation techniques. The antibodies were tested on skin biopsy sections from healthy controls, from CF patients homozygous for the most common mutation, DeltaF508, and from patients carrying two nonsense mutations. Of the eight CFTR antibodies, only three-M3A7, MATG 1104, and cc24-met the criteria necessary for immunolocalization of CFTR in sweat glands. The labeling pattern in the CF sweat glands was consistent with the postulated processing defect of DeltaF508 CFTR. The antibodies exhibited different sensitivities for detecting DeltaF508 CFTR.
Acetone↗
Categories of deltaF508 homozygous cystic fibrosis twin and sibling pairs with distinct phenotypic characteristics.
Cystic fibrosis (CF), the most common severe autosomal recessive trait among Caucasians, is caused by molecular lesions in the cystic fibrosis transmembrane conductance regulator gene (CFTR). The course of the multi-organ disease CF is highly variable, suggesting the influence of environmental factors and/or modulating genes other than CFTR on the disease phenotype. To evaluate the cause of CF disease variability, the European CF Twin and Sibling Study collected data on two clinical parameters most sensitive for the course and prognosis of CF, ie weight predicted for height (wfh)% (representative for the nutritional status) and FEVPerc (representative for the pulmonary status) for a cohort of 277 sibling pairs, 12 pairs of dizygous twins and 29 pairs of monozygous twins. Of these 318 CF twin and sib pairs, 114 were reported to be homozygous for the most frequent CF disease-causing lesion, deltaF508. Intra-pair discordance was assessed by the intra-pair differences with wfh% and FEVPerc and by DELTA, a composite parameter defined by linear combination of wfh% and FEVPerc in order to describe discordance with respect to the overall disease severity. Monozygous twins had a significantly lower DELTA than dizygous twins (P = 0.05) indicating that CF disease severity is modulated by an inherited component in addition to the CFTR gene itself. Extreme phenotypes are considered to be more informative for the analysis of any quantitative trait. Thus, we aimed to quantify disease severity and intra-pair discordance in order to select pairs with the extreme phenotypes DIS (discordant patient pairs), CON+ (concordant and mildy affected patient pairs) and CON- (concordant and severely affected patient pairs). The algorithm reliably discriminated between pairs DIS, CON+ and CON- among the cohort of deltaF508 homozygotes. The selected pairs from these categories demonstrated non-overlapping properties for wfh%, FEVPerc and the intra-pair difference of both parameters.
Adolescent↗
DeltaF508 CFTR protein expression in tissues from patients with cystic fibrosis.
Heterologous expression of the cystic fibrosis transmembrane conductance regulator (CFTR) provided evidence that the major cystic fibrosis (CF) mutation DeltaF508 leads to defective protein folding in the endoplasmic reticulum, which prevents its processing and targeting to the cell surface. In this study, we investigated endogenous CFTR expression in skin biopsies and respiratory and intestinal tissue specimens from DeltaF508 homozygous and non-CF patients, using immunohistochemical and immunoblot analyses with a panel of CFTR antibodies. CFTR expression was detected at the luminal surface of reabsorptive sweat ducts and airway submucosal glands, at the apex of ciliated cells in pseudostratified respiratory epithelia and of isolated cells of the villi of duodenum and jejunum, and within intracellular compartments of intestinal goblet cells. In DeltaF508 homozygous patients, expression of the mutant protein proved to be tissue specific. Whereas DeltaF508 CFTR was undetectable in sweat glands, the expression in the respiratory and intestinal tracts could not be distinguished from the wild-type by signal intensity or localization. The tissue-specific variation of DeltaF508 CFTR expression from null to apparently normal amounts indicates that DeltaF508 CFTR maturation can be modulated and suggests that determinants other than CFTR mislocalization should play a role in DeltaF508 CF respiratory and intestinal disease.
Amino Acid Sequence↗
Cystic fibrosis: an inherited susceptibility to bacterial respiratory infections.
Cystic fibrosis is a severe monogenic disorder of ion transport in exocrine glands. The basic defect predisposes to chronic bacterial airway infections with Staphylococcus aureus, Haemophilus influenzae, Pseudomonas aeruginosa and Burkholderia cepacia. The Pseudomonas infections in cystic fibrosis are a paradigm of how versatile environmental bacteria can conquer, adapt and persist in an atypical habitat and successfully evade defence mechanisms and chemotherapy in a susceptible host. Regular chemotherapy with aerosol and systemic antipseudomonal drugs has improved the course and prognosis of the disease, and research for effective vaccines is on the way.
Bacterial Infections↗
Iodomycin and iodipine, a structural analogue of azidopine, bind to a common domain in hamster P-glycoprotein.
Both the overexpression of P-glycoprotein and the broad range of substrates of this ATP-binding cassette (ABC) transporter induce the phenomenon of multidrug resistance, one major cause of the failure of cancer chemotherapy in humans. This study reports that [125I]iodipine, a structural analogue of the 1,4-dihydropyridine azidopine, shares a common binding site with iodomycin, a Bolton-Hunter derivative of the anthracycline daunomycin. This binding site is different from that described for iodoarylazidoprazosin, which is presumed to share a common binding site with azidopine. Edman sequencing revealed that [125I]iodipine had photolabelled the same peptide as iodomycin and spans the primary sequence of hamster isoform pgp1 from amino acid 230 to amino acid 312.
ATP Binding Cassette Transporter, Subfamily B, Mem↗
Small-colony variants of Pseudomonas aeruginosa in cystic fibrosis.
In the context of chronic lung infection due to Pseudomonas aeruginosa in cystic fibrosis (CF), attention has been focused on the presence of the most common mucoid phenotype. In this study, the presence of small-colony variants (SCVs) of P. aeruginosa in respiratory tract specimens from patients with CF was investigated, and the clinical conditions predisposing to SCVs were analyzed. P. aeruginosa SCVs were isolated from 33 of 86 P. aeruginosa-positive CF patients over a 2-year period. Fast-growing revertants with larger surface colonies could be isolated from SCV populations. Electron microscopy revealed no significant difference in cell size or morphology. MICs of a broad range of antipseudomonas agents for SCVs were two- to eightfold higher than values for revertants. Recovery of SCVs was correlated with parameters revealing poor lung function and was significantly associated with daily inhalation of tobramycin or colistin.
Adolescent↗
Identification of Burkholderia spp. in the clinical microbiology laboratory: comparison of conventional and molecular methods.
Cystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situation is not in the least due to the poorly defined taxonomic status of these bacteria, and further validation of the available diagnostic assays is required. A total of 114 geographically diverse bacterial isolates, previously identified in reference laboratories as Burkholderia cepacia (n = 51), B. gladioli (n = 14), Ralstonia pickettii (n = 6), B. multivorans (n = 2), Stenotrophomonas maltophilia (n = 3), and Pseudomonas aeruginosa (n = 11), were collected from environmental, clinical, and reference sources. In addition, 27 clinical isolates putatively identified as Burkholderia spp. were recovered from the sputum of Dutch CF patients. All isolates were used to evaluate the accuracy of two selective growth media, four systems for biochemical identification (API 20NE, Vitek GNI, Vitek NFC, and MicroScan), and three different PCR-based assays. The PCR assays amplify different parts of the ribosomal DNA operon, either alone or in combination with cleavage by various restriction enzymes (PCR-restriction fragment length polymorphism [RFLP] analysis). The best system for the biochemical identification of B. cepacia appeared to be the API 20NE test. None of the biochemical assays successfully grouped the B. gladioli strains. The PCR-RFLP method appeared to be the optimal method for accurate nucleic acid-mediated identification of the different Burkholderia spp. With this method, B. gladioli was also reliably classified in a separate group. For the laboratory diagnosis of B. cepacia, we recommend parallel cultures on blood agar medium and selective agar plates. Further identification of colonies with a Burkholderia phenotype should be performed with the API 20NE test. For final confirmation of species identities, PCR amplification of the small-subunit rRNA gene followed by RFLP analysis with various enzymes is recommended.
Bacterial Typing Techniques↗
Clinical presentation of exclusive cystic fibrosis lung disease.
The diagnosis of cystic fibrosis (CF) is based on the occurrence of two mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and on assays that measure the basic defect of abnormal chloride transport in the affected organs. However, in cases of atypical CF not all diagnostic tests may be positive. We present a patient with an atypical CF phenotype in whom the only presenting symptom was severe CF-like lung disease substantiated by an abnormal nasal potential difference. Genetic analysis showed that the patient was a symptomatic heterozygote, which suggests that one lesion in the CFTR gene may be sufficient to cause CF-like lung disease.
Adult↗
The golden age of bacterial genomics.
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Genome, Bacterial↗
Cloning of prokaryotic genomes in yeast artificial chromosomes: application to the population genetics of Pseudomonas aeruginosa.
Yeast artificial chromosomes (YACs) can accommodate large inserts and hence should be attractive tools for intra- and interspecies comparisons of bacterial genomes. YAC libraries were constructed from size-selected partial digests of human and Pseudomonas aeruginosa PAO DNA and SpeI-restricted PAO DNA. Whereas YACs from human DNA had an average size of 350 kilobase pairs (kbp), a P. aeruginosa sequence larger than 120 kbp was absent or truncated in the eukaryotic host. Coligation occurred for YACs smaller than 40 kbp, but stable YACs with 40-120 kbp large inserts of P. aeruginosa DNA were obtained in high yield. SpeI-restricted chromosomes from 97 P. aeruginosa strains representing 47 genotypes were hybridized with stable YACs from three equidistant regions of the PAO genome. The low complexity of hybridizing bands demonstrated that the analyzed 100 kbp sequence contigs were stably maintained in most P. aeruginosa isolates from both disease and environmental habitats.
Chromosomes, Artificial, Yeast↗
Smith/Birnstiel mapping of genome rearrangements in Pseudomonas aeruginosa.
A novel application of the Smith/Birnstiel technique is presented for the analysis of intraspecies genomic diversity in small genomes. Rare-cutter total/N frequent-cutter partial restriction digestions are separated in N separate lanes by pulsed-field gel electrophoresis, blotted and hybridized with rare-cutter fragment ends as probes. The evaluation of the autoradiogram results in high-resolution restriction maps of 10-200 kbp regions. The technique was applied to the analysis of genome rearrangements in Pseudomonas aeruginosa strains. Comparison of the region encoding the tryptophan biosynthesis genes in the PAO and the IATS serotype 5 strains revealed that shared sequence characterized by almost identical restriction fingerprints was interrupted in the serotype 5 strain by small islands displaying strain-specific restriction site signatures. A multistep rearrangement in a hypervariable chromosome region downstream of the phn locus was detected in serial airway isolates from a patient with cystic fibrosis.
Chromosomes, Artificial, Yeast↗
Differential genome analysis of bacteria by genomic subtractive hybridization and pulsed field gel electrophoresis.
A comprehensive analysis of the differences between the genomes of two closely related bacterial strains should give insight into the molecular basis of their individual phenotypic and genotypic characteristics. Here we present an integrative approach including two different strategies for the thorough investigation of genomic divergence. We have combined two techniques including genomic subtractive hybridization and comparative genome mapping by pulsed field gel electrophoresis (PFGE) techniques. The subtractive method for which a protocol is given herein results in the production of a library of specific DNA sequence tags present only in one strain, while the construction of macrorestriction maps of the bacterial chromosomes yields data about the overall genome organization and the arrangement and distance of gene loci. Comparison of the physical and genetic maps and determination of the map positions of the strain-specific DNA sequences reveals gross chromosomal modifications, insertions or deletions of additional genetic material, and transpositional events. The further investigation of the strain-specific regions yields information about the nature and origin of the acquired DNA and their influence on the evolution of the individual bacterial genome. The two methods were applied to differential genome analysis of clonal divergence in Pseudomonas aeruginosa choosing two clone C isolates from diverse habitats.
Chromosomes, Bacterial↗
Structural and functional implications of sequence diversity of Pseudomonas aeruginosa genes oriC, ampC and fliC.
Sequence analysis of three representative gene loci, oriC, ampC and fliC, in 19 Pseudomonas aeruginosa strains revealed a low sequence diversity that does not correlate with the extensive diversity of P. aeruginosa habitats. Single point mutations lead to a mean sequence diversity of 0.40%, 0.38% and 0.59% for oriC, ampC and a-type fliC, respectively, but of only 0.05% for b-type flagellin genes. The analyzed genes encode highly conserved functions that are subject to strong selective pressure. The detected nucleotide substitutions of oriC, accumulating in a central 95 bp region, affect neither the putative DnaA binding sites nor the 13 bp direct repeats that presumably provide the sites to open oriC duplex DNA. Even in P. aeruginosa strain DSM 1128, which exhibits an unusually high sequence variability in several analyzed genes, the 9 bp and 13 bp motifs are conserved, reflecting their essential functional role in replication initiation. The two flagellin types, differing by 37-38% in their primary structure, exhibit pronounced structural and functional homology, as shown by alignment of flagellin variants by hydrophobicity index, probability of surface exposure, chain flexibility and antigenicity, and by cross-reactivity between both proteins using specific antisera. Five nonsynonymous nucleotide substitutions of ampC lead to beta-lactamase variants that differ in recognition and turnover of substrate, as deduced from the three-dimensional structure of the highly homologous Enterobacter cloacae beta-lactamase and confirmed by inhibition kinetics. The identified point mutations in the three genes are classified as selectively equivalent sequence variants indicating neutral genetic drift as a mechanism of molecular evolution in P. aeruginosa, rather than positive selection.
Bacterial Proteins↗
Cystic-fibrosis-like disease unrelated to the cystic fibrosis transmembrane conductance regulator.
Cystic fibrosis (CF) is considered to be a monogenic disease caused by molecular lesions within the cystic fibrosis transmembrane conductance regulator (CFTR) gene and is diagnosed by elevated sweat electrolytes. We have investigated the clinical manifestations of cystic fibrosis, CFTR genetics and electrophysiology in a sibpair in which the brother is being treated as having CF, whereas his sister is asymptomatic. The diagnosis of CF in the index patient is based on highly elevated sweat electrolytes in the presence of CF-related pulmonary symptoms. The investigation of chloride conductance in respiratory and intestinal tissue by nasal potential difference and intestinal current measurements, respectively, provides no evidence for CFTR dysfunction in the siblings who share the same CFTR alleles. No molecular lesion has been identified in the CFTR gene of the brother. Findings in the investigated sibpair point to the existence of a CF-like disease with a positive sweat test without CFTR being affected. Other factors influencing sodium or chloride transport are likely to be the cause of the symptoms in the patient described.
Adult↗
ATP depletion induces a loss of respiratory epithelium functional integrity and down-regulates CFTR (cystic fibrosis transmembrane conductance regulator) expression.
To mimic the effect of ischemia on the integrity of airway epithelium and expression of cystic fibrosis transmembrane conductance regulator (CFTR), we induced an ATP depletion of the respiratory epithelium from upper airway cells (nasal tissue) and human bronchial epithelial 16HBE14o- cell line. Histological analysis showed that 2 h of ATP depletion led to a loss of the epithelium integrity at the interface between basal cells and columnar cells. The expression of connexin 43 (Cx43, subunit of the gap junctions) and desmoplakins 1 and 2 (DPs 1 and 2, major components of the desmosomes) proteins was inhibited. After 90 min of ATP depletion, a significant decrease of the transepithelial resistance (25%) was observed but was reversible. Similar results were obtained with the 16HBE14o- human bronchial epithelial cell line. ATP depletion led to actin filaments depolymerization. The expression of the mature CFTR (170 kDa) and fodrin proteins at the apical domain of the ciliated cells was down-regulated. The steady-state levels of CFTR, Cx43, DPs 1 and 2 mRNAs, semiquantified by RT-polymerase chain reaction kinetics, remained constant throughout ATP depletion in nasal tissue as in the homogeneous cell population of 16HBE14o- human bronchial epithelial cell line. This suggests that the down-regulation of these proteins might be posttranscriptional. The intercellular diffusion through gap junctions of Lucifer dye was completely inhibited after 90 min of ATP depletion but was reversible. The volume-dependent and the cAMP-dependent chloride secretion were inhibited in a nonreversible way. Taken together, these results suggest that an ATP depletion in human airway epithelium, mimicking ischemia, may induce a marked alteration in the junctional complexes and cytoskeleton structure concomitantly with a loss of apical CFTR expression and chloride secretion function.
Adenosine Triphosphate↗
Large genome rearrangements discovered by the detailed analysis of 21 Pseudomonas aeruginosa clone C isolates found in environment and disease habitats.
In order to determine primary genetic events which occur during the diversification of a Pseudomonas aeruginosa clone in natural habitats, comparative genome analysis of 21 isolates of a predominant clone, called clone C, derived mainly from patients with cystic fibrosis (CF) and the aquatic environment, was carried out. Physical chromosome maps were constructed for the restriction enzymes SpeI, PacI, SwaI and I-CeuI by one and two-dimensional pulsed-field gel electrophoresis and by comparison with the existing strain C map. The positioning of 26 genes generated the genetic maps. Chromosome size varied between 6345 and 6606 kilobase-pairs (kb). A plasmid of 95 kb was detected in the strains of non-CF origin and, in addition, was found to be integrated into the chromosome of all strains but one CF isolate. Four subgroups of clone C strains were discriminated by the acquisition and loss of large blocks of DNA that could cover more than 10% of the chromosome size. The exchange of DNA blocks which ranged in size from 1 kb to 214 kb occurred preferentially around the terminus of replication region which is poor in biosynthetic genes. Genetic material which was additionally introduced into strain C in comparison with strain PAO seems to be a target of mutational processes in clone C strains. Within and among subgroups CF isolates frequently exhibited large inversions affecting the whole chromosomal structure. We concluded that the exchange of DNA blocks by mechanisms of horizontal transfer and large chromosomal inversions are major factors leading to the divergence of a clone in the species P. aeruginosa.
Chromosome Mapping↗