Identification of DNA gyrase A mutations in ciprofloxacin-resistant isolates of Salmonella typhimurium from men and cattle in Germany.

Six multiply resistant isolates of Salmonella typhimurium var. copenhagen with high-level resistance to fluoroquinolones (e.g., MIC of ciprofloxacin: 32 micrograms/ml) were isolated from human patients (n = 3) and from cattle (n = 3). The isolates were examined by complementation tests using a set of broad-host-range plasmids, which carry either the gyrA+ or the gyrB+ genes or a combination of both from Escherichia coli K-12. The results indicated a combination of gyrA and gyrB mutations in all isolates. Subsequent direct sequencing of PCR-generated internal DNA fragments of gyrA revealed an identical double mutation in all six isolates (Ser-83-->Ala and Asp-87-->Asn). In addition, the results of phenotypic (i.e., phagetype, biotype, serotype) and genotypic characterization [i.e., ribotyping and polymerase chain reaction fingerprinting (PCR-fingerprinting)] were identical for all six isolates and were distinguishable from a quinolone-susceptible strain of the same serovar and an unrelated isolate of S. typhimurium. These data indicate the clonal identity of the fluoroquinolone-resistant strains of S. typhimurium isolated from men and cattle in Germany.

Identification and DNA sequence analysis of 15 new alpha 1-antitrypsin variants, including two PI*Q0 alleles and one deficient PI*M allele.

We have investigated the molecular basis of 15 new alpha 1-antitrypsin (alpha 1AT) variants. Phenotyping by isoelectric focusing (IEF) was used as a screening method to detect alpha 1AT variants at the protein level. Genotyping was then performed by sequence analysis of all coding exons, exon-intron junctions, and the hepatocyte-specific promoter region including exon Ic. Three of these rare variants are alleles of clinical relevance, associated with undetectable or very low serum levels of alpha 1AT:the PI*Q0saarbruecken allele generated by a 1-bp C-nucleotide insertion within a stretch of seven cytosines spanning residues 360-362, resulting in a 3' frameshift and the acquisition of a stop codon at residue 376; a point mutation in the PI*Q0lisbon allele, resulting in a single amino acid substitution Thr68(ACC)-->Ile(ATC); and an in-frame trinucleotide deletion delta Phe51 (TTC) in the highly deficient PI*Mpalermo allele. The remaining 12 alleles are associated with normal alpha 1AT serum levels and are characterized by point mutations causing single amino acid substitutions in all but one case. This exception is a silent mutation, which does not affect the amino acid sequence. The limitation of IEF compared with DNA sequence analysis, for identification of new variants, their generation by mutagenesis, and the clinical relevance of the three deficiency alleles are discussed.

A leucine-to-proline substitution causes a defective alpha 1-antichymotrypsin allele associated with familial obstructive lung disease.

Using denaturing gradient gel electrophoresis and direct sequencing of amplified genomic DNA, we have identified two defective mutants of the human alpha 1-antichymotrypsin (ACT) gene associated with chronic obstructive pulmonary disease (COPD). A leucine 55-to-proline substitution causing a defective ACT allele (Bochum-1) was observed in a family with COPD in three subsequent generations. Another mutation, proline 229-to-alanine (Bonn-1), was associated with ACT serum deficiency in four patients with a positive family history. These mutations were not detected among 100 healthy control subjects, suggesting a possible pathogenetic role of ACT gene defects in a subset of patients with COPD.

The molecular basis of alpha 1-antichymotrypsin deficiency in a heterozygote with liver and lung disease.

Alpha 1-antichymotrypsin (alpha 1-ACT) is a serine proteinase inhibitor (serpin) with cathepsin G, mast cell chymase and chymotrypsin as target enzymes. We present the case of a middle-aged man with low plasma levels of alpha 1-ACT, asthma with progression to emphysema, and chronic HCV positive liver disease with selective accumulation of alpha 1-ACT in hepatocytes. This secretory defect is analogous to that seen in Pi Z alpha 1-antitrypsin deficiency. The molecular basis of alpha 1-ACT deficiency in this patient has been characterized by direct sequencing of the alpha 1-ACT genes from the patient and his father. A C-->G transversion in exon III causing a 229Pro-->Ala substitution is proposed to cause a conformational change resulting in abnormal transport through the RER. This mutation was found in one of 20 additional tested patients with chronic obstructive lung disease, but in no control. Two additional polymorphisms of the gene have been identified in unrelated healthy individuals with normal plasma alpha 1-ACT levels. The alpha 1-ACT deficiency state may predispose to obstructive lung disease and influence the course of liver disease. Identification of a specific mutation allows identification of heterozygotes for this deficiency allowing future evaluation of its clinical significance.

Improved phenotyping of alpha 1-antichymotrypsin (ACT) by isoelectric focusing and immunoprinting: first demonstration of a deficient protein variant in the ACT system.

Genetic variation of human alpha 1-antichymotrypsin (ACT) was investigated in sera using thin-layer polyacrylamide gel isoelectric focusing (pH range 4.0-6.5) followed by immunoprinting with a monospecific anti-human ACT antibody. Sialidase-treated samples showed a microheterogeneous banding pattern which consisted of two major and several additional minor components with isoelectric points between pH 5.0 and 5.3. A population study of 200 unrelated individuals from southern Germany revealed no genetic variation. In a clinical investigation, however, we found a unique banding pattern in a female patient suffering from chronic obstructive pulmonary disease. In comparison with the monomorphic normal type the detected variant phenotype shows two additional bands that have lower intensities and are located cathodically to their major bands. Inheritance of the deficient IEF variant "ACT Bochum" was confirmed by a family study. To our knowledge this is the first genetic ACT mutant to be observed at the protein level.

Cloning of the human alpha 2-macroglobulin gene and detection of mutations in two functional domains: the bait region and the thiolester site.

Overlapping genomic clones of the human alpha 2-macroglobulin (alpha 2M) gene were isolated from a cosmid library and were used to map 80 kb of the chromosomal region of this gene. Fragments carrying the two exons encoding the bait region and the exon encoding the thiolester site were partially sequenced and PCR primers were designed for the amplification of both functional domains. By direct genomic sequencing of these domains in 30 healthy individuals and in 30 patients with chronic lung disease three mutations were detected. The first was a sequence polymorphism occurring near the thiolester site of the gene, changing Val1000 (GTC) to Ile1000 (ATC), with allele frequencies of 0.30 (GTC) and 0.70 (ATC), respectively. No difference of alpha 2M serum levels was observed for these two alleles. The second mutation occurred within the thiolester site of one patient, changing Cys972(TGT) to Tyr972(TAT). Since activation of the internal thiolester formed between Cys972 and Gln975 in each of the subunits of the tetrameric alpha 2M is involved in the covalent cross-linking of the activating proteinase, this mutation is predicted to interfere with alpha 2M function. The alpha 2M serum level was within the normal range in this patient. In one healthy individual we detected an alteration of the bait region sequence, which is usually encoded by two different exons separated by an intron of size 1.6 kb. In this individual, PCR amplification of genomic DNA using the bait region primers produced the common fragment of size 1.8 kb and an additional variant fragment of size 0.23 kb. This finding, and the genomic sequencing data of this individual, indicate that he carries two different alleles of the alpha 2M gene: one with the regular structure (bait exon I-intron-bait exon II), the other with the two bait exons fused into one. Direct genomic sequencing of the two alpha 2M functional domains is a useful tool for the detection of the genetic, and possibly the functional, heterogeneity of alpha 2M. This, in turn, may provide some insight into the hitherto unknown physiological role(s) of alpha 2M, by studying in vivo effects of naturally occurring mutations of the gene.

Sequence analysis of the cystic fibrosis gene in patients with disseminated bronchiectatic lung disease. Application in the identification of a cystic fibrosis patient with atypical clinical course.

The diagnosis of classical cystic fibrosis (CF) is easily made by clinical assessment alone, but may be missed or delayed in cases with an atypical clinical course. In a recent major study the age at diagnosis varied between 2 months and 47 years. For diagnostic purposes we have investigated the cystic fibrosis transmembrane regulator (CFTR) gene in 10 adult patients (age 18 to 45 years) with chronic obstructive pulmonary disease since childhood or adolescence and bronchiectases disseminated through both lungs. Only one subject (a 29-year-old male) had exocrine pancreatic insufficiency (PI); all others were pancreatic-sufficient (PS). The first nucleotide (ATP)-binding fold of the CFTR was analyzed by direct sequencing of polymerase chain reaction (PCR)-amplified genomic DNA in these cases. Two patients with different phenotypes (one PI, one PS) were found to be homozygous for the common delta F508 mutation of the CFTR gene, which proved the diagnosis of cystic fibrosis in their cases and allowed genetic counselling. The PS patient had normal sweat tests and had not previously been recognized as having CF. Four other patients were heterozygous for delta F508, with no other mutation in exons 10 or 11 of the gene, and four patients had normal sequences of these exons. Because only about 70% of all CF chromosomes carry delta F508, the unexpectedly high frequency (4/8 = 50%) of heterozygosity for delta F508 among the non-delta F508/delta F508 patients with bronchiectases suggests that some of these might also have unrecognized CF with rare genotypes and mutations in any of the 22 exons not sequenced.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA polymorphisms associated with a new alpha 1-antitrypsin PIQ0 variant (PIQ0riedenburg).

A new PIQ0 variant (PIQ0riedenburg) is described; it is caused by a complete deletion of the alpha 1-antitrypsin (alpha 1 AT) gene. The deletion gives rise to four new restriction fragment length polymorphisms (RFLPs) detected with a genomic probe of the 5' region of the gene. Analysis of the RFLPs indicates that the deletion starts immediately upstream of exon Ic. The deletion extends into the 3' flanking region of the gene but does not include the alpha 1 AT-related gene (the PIL gene), which is located 12 kb downstream of the alpha 1 AT gene.

Highly variable clinical course in severe alpha 1-antitrypsin deficiency--use of polymerase chain reaction for the detection of rare deficiency alleles.

Among 20 individuals with severe alpha 1-antitrypsin (alpha 1AT) deficiency we observed extremely variable clinical phenotypes ranging from rapidly progressive lung disease fatal at the age of 42 years to an asymptomatic individual with normal lung function at the age of 50 years. Eighteen subjects, including the asymptomatic one, carried the deficient Pi ZZ phenotype as determined by isoelectric focusing (IEF). Their mean alpha 1AT serum level was 36.7 +/- 7.7 mg/dl. DNA restriction analysis showed that all of them had the classical Pi Z-allele-associated DNA haplotype, thus confirming the IEF data. Obviously not all Pi ZZ individuals will have clinical sequelae caused by this genotype. The important differences in clinical course observed could not be explained by smoking habits alone. Probably additional factors are pertinent to the pathogenesis of the lung disease associated with alpha 1AT deficiency (defects in other genes, environmental influences other than smoking). In two patients with very low alpha 1AT serum levels definitive phenotyping by IEF was not possible. Therefore we investigated the molecular basis of their deficiency using polymerase chain reaction (PCR) amplification of the coding exons of their alpha 1AT genes and direct sequencing of the amplification products. Sequence data analysis showed that one of these patients, who had initially been phenotyped as Pi ZZ by IEF, had in fact the genotype Pi QObellinghamZ, thus explaining her low alpha 1AT serum level of 20 mg/dl. The other patient (alpha 1AT serum level 3.7 mg/dl) exhibited the rare genotype Pi MheerlenQOgranite falls. Despite his nearly complete alpha 1AT deficiency, he suffered from only moderately severe pulmonary disease at the age of 42 years.

Sequence data of the rare deficient alpha 1-antitrypsin variant PI Zaugsburg.

Weidinger et al. recognized a rare deficient PI-variant, named PI Zaugsburg (PI Zaug), by using isoelectric focusing with a narrow pH gradient. The serum alpha 1-antitrypsin (alpha 1AT) level determined quantitatively in an individual carrying the phenotype PI M1Zaug revealed a value of 50%-60% of the normal range. The frequency of the deficient PI*Zaug allele is still unknown. Haplotyping the Zaug-affected chromosome, we found a pattern different from the common PI*Z allele described by Cox et al. Therefore, we directly sequenced the coding exons of both genes (M1 and Zaug) after PCR amplification. Zaug sequence data analysis showed the presence of the common PI*Z allele-specific mutation (M1 Glu342 GAG to Z Lys342 AAG) surprisingly occurring in an M2 ancestral gene. This is not consistent with the heretofore common finding, by Nukiwa et al. and others, that this mutation is derived from an M1 (Ala213) background gene. No further mutations were found in the PI Zaug gene.