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PubMed1991

p-cresol methylhydroxylase from a denitrifying bacterium involved in anaerobic degradation of p-cresol.

A bacterium, strain PC-07, previously isolated as part of a coculture capable of growing on p-cresol under anaerobic conditions with nitrate as the acceptor was identified as an Achromobacter sp. The first enzyme of the pathway, p-cresol methylhydroxylase, which converts its substrate into p-hydroxybenzyl alcohol, was purified. The enzyme had an Mr of 130,000 and the spectrum of a flavocytochrome. It was composed of flavoprotein subunits of Mr 54,000 and cytochrome subunits of Mr 12,500. The midpoint redox potential of the cytochrome was 232 mV. The Km and kcat for p-cresol were 21 microM and 112 s-1 respectively, and the Km for phenazine methosulfate, the artificial acceptor used in the assays, was determined to be 1.7 mM. These properties place the enzyme in the same class as the p-cresol methylhydroxylases from aerobically isolated Pseudomonas spp.

Alcaligenes↗
PubMed1994

Purification and characterization of Clostridium perfringens 120-kilodalton collagenase and nucleotide sequence of the corresponding gene.

Clostridium perfringens type C NCIB 10662 produced various gelatinolytic enzymes with molecular masses ranging from approximately 120 to approximately 80 kDa. A 120-kDa gelatinolytic enzyme was present in the largest quantity in the culture supernatant, and this enzyme was purified to homogeneity on the basis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified enzyme was identified as the major collagenase of the organism, and it cleaved typical collagenase substrates such as azocoll, a synthetic substrate (4-phenylazobenzyloxy-carbonyl-Pro-Leu-Gly-Pro-D-Arg [Pz peptide]), and a type I collagen fibril. In addition, a gene (colA) encoding a 120-kDa collagenase was cloned in Escherichia coli. Nested deletions were used to define the coding region of colA, and this region was sequenced; from the nucleotide sequence, this gene encodes a protein of 1,104 amino acids (M(r), 125,966). Furthermore, from the N-terminal amino acid sequence of the purified enzyme which was found in this reading frame, the molecular mass of the mature enzyme was calculated to be 116,339 Da. Analysis of the primary structure of the gene product showed that the enzyme was produced with a stretch of 86 amino acids containing a putative signal sequence. Within this stretch was found PLGP, the amino acid sequence constituting the Pz peptide. This sequence may be implicated in self-processing of the collagenase. A consensus zinc-binding sequence (HEXXH) suggested for vertebrate Zn collagenases is present in this bacterial collagenase. Vibrio alginolyticus collagenase and Achromobacter lyticus protease I showed significant homology with the 120-kDa collagenase of C. perfringens, suggesting that these three enzymes are evolutionarily related.

Amino Acid Sequence↗
PubMed1994

Cloning and nucleotide sequence analysis of the colH gene from Clostridium histolyticum encoding a collagenase and a gelatinase.

The colH gene encoding a collagenase was cloned from Clostridium histolyticum JCM 1403. Nucleotide sequencing showed a major open reading frame encoding a 116-kDa protein of 1,021 amino acid residues. The deduced amino acid sequence contains a putative signal sequence and a zinc metalloprotease consensus sequence, HEXXH. A 116-kDa collagenase and a 98-kDa gelatinase were copurified from culture supernatants of C. histolyticum. While the former degraded both native and denatured collagen, the latter degraded only denatured collagen. Peptide mapping with V8 protease showed that all peptide fragments, except a few minor ones, liberated from the two enzymes coincided with each other. Analysis of the N-terminal amino acid sequence of the two enzymes revealed that their first 24 amino acid residues were identical and coincided with those deduced from the nucleotide sequence. These results indicate that the 98-kDa gelatinase is generated from the 116-kDa collagenase by cleaving off the C-terminal region, which could be responsible for binding or increasing the accessibility of the collagenase to native collagen fibers. The role of the C-terminal region in the functional and evolutional aspects of the collagenase was further studied by comparing the amino acid sequence of the C. histolyticum collagenase with those of three homologous enzymes: the collagenases from Clostridium perfringens and Vibrio alginolyticus and Achromobacter lyticus protease I.

Amino Acid Sequence↗
PubMed1996

A substitution at His-120 in the LasA protease of Pseudomonas aeruginosa blocks enzymatic activity without affecting propeptide processing or extracellular secretion.

The LasA protease of Pseudomonas aeruginosa can degrade elastin and is an important contributor to the pathogenesis of this organism. LasA (20 kDa) is a member of the beta-lytic endopeptidase family of extracellular bacterial proteases, and it shows high-level staphylolytic activity. We sequenced the lasA gene from strain FRD1 and overexpressed it in Escherichia coli. The lasA gene encodes a precursor, known as pre-proLasA, of 45,582 Da. Amino-terminal sequence analysis allowed the identification of the signal peptidase cleavage site and revealed that the 31-amino-acid signal peptide was removed in E. coli. The remaining proLasA (42 kDa) did not undergo autoproteolytic processing and showed little staphylolytic activity. However, it was readily processed to a 20-kDa active staphylolytic protease by incubation with trypsin or with the culture filtrate of a P. aeruginosa lasAdelta mutant. Thus, removal of the propeptide (22 kDa) was required to convert proLasA into an active protease. Although LasA protease was critical for staphylolytic activity, other proteases like elastase were found to enhance staphylolysis. Under the control of an inducible trc promoter, lasA was overexpressed in P. aeruginosa and the processing intermediates were examined. Compared with wild-type cells, the overproducing cells accumulated more 42-kDa proLasA species, and the culture supernatants of the overproducing cells showed increased levels of active 20-kDa LasA protease. Small amounts of a 25-kDa extracellular LasA-related protein, which could represent a potential processing intermediate, were also observed. To better understand the structure-function relationships in LasA protease, we tested whether His-120-X-His-122 in the mature portion of LasA plays a role in activity. This motif and surrounding sequences are conserved in the related beta-lytic protease of Achromobacter lyticus. Oligonucleotide-directed mutagenesis was used to change His-120 to Ala-120, thus forming the lasA5 allele. The product of lasA5 expressed from the chromosome of P. aeruginosa was processed to a stable, secreted 20-kDa protein (designated LasA-H120A) which was devoid of staphylolytic activity. This suggests that His-120 is essential for LasA activity and favors the possibility that proLasA processing and secretion in P. aeruginosa can proceed via mechanisms which do not involve autoproteolysis.

Amino Acid Sequence↗
PubMed1962

BACTERIAL OXIDATION OF DIPICOLINIC ACID I. : Isolation of Microorganisms, Their Culture Conditions, and End Products.

Arima, Kei (University of Tokyo, Tokyo, Japan) and Yasuo Kobayashi. Bacterial oxidation of dipicolinic acid. I. Isolation of microorganisms, their culture conditions, and end products. J. Bacteriol. 84:759-764. 1962.-In a study of the metabolic pathway(s) of dipicolinic acid (DPA) in microorganisms, 436 strains of soil microorganisms were isolated by use of an enrichment culture technique. Most of them were bacteria, and one of them, Achromobacter, which had the strongest DPA-oxidizing activity, was used for the following experiments. In DPA-free medium, the enzymes which oxidize DPA were not produced. The best culture condition for enzyme production and cell growth was: Nutrient Broth supplemented with 0.1% DPA, 30 C, and 20 hr of shake culture. End products were oxalic acid, NH(3), and CO(2). Oxalic acid was not oxidized further by this bacterium. The over-all reaction equation of DPA oxidation was determined.

Journal Article↗
PubMed1966

Bacterial nutritional approach to mechanisms of oxygen toxicity.

Gottlieb, Sheldon F. (Union Carbide Corp., Tonawanda, N.Y.). Bacterial nutritional approach to mechanisms of oxygen toxicity. J. Bacteriol. 92:1021-1027. 1966.-Inhibition by oxygen of growth of the bacterium Achromobacter P6 was reversed by amino acid supplements. The reversal of oxygen-induced growth inhibition was not due to the presence of reducing substances in the growth medium. Oxygen primarily exerts a bacteriostatic effect. The oxygen inhibition of growth occurred over a wide pH range. Oxygen inhibition of growth was observed when 1-amino-2-propanol, acetate, lactate, citrate, or glucose was used as the sole source of carbon and energy. No inhibition of growth was obtained when succinate, fumarate, malate, or glutamate was used as the source of carbon and energy. Oxygen markedly depressed the respiration of P6 when 1-amino-2-propanol was the substrate. There was no depression of respiration under oxygen with succinate as substrate. P6 grown in the presence of high oxygen tensions had a higher rate of respiration under oxygen than similar air-grown cells. Chloramphenicol did not affect the rate of oxygen consumption or cause a further depression of the respiratory rate in the presence of oxygen. It is suggested that microbes may serve as a model system for studying the cellular and subcellular mechanisms of oxygen toxicity.

1-Propanol↗
PubMed1982

Accuracy of a rapid carbohydrate oxidation microtube method for identification of nonfermentative gram-negative bacilli.

A rapid carbohydrate oxidation microtube system (Carr Microbiologicals, Wichita, Kans.), designed for detecting the saccharolytic activity of gram-negative, nonfermenting bacilli, was evaluated and compared with the conventional oxidation-fermentation method. The oxidation of glucose, maltose, lactose, and xylose was tested with 430 strains of Pseudomonas, Acinetobacter, Achromobacter, Alcaligenes, Moraxella, Flavobacterium, and Bordetella species. More than 95% of the isolates tested gave correct oxidation reactions within 4 h in the rapid carbohydrate oxidation microtubes, whereas oxidation-fermentation media required 24 h to achieve the same sensitivity. The microtube system was found to be simple, accurate, rapid, and economical.

Bacteriological Techniques↗
PubMed1982

Growth of non-Campylobacter, oxidase-positive bacteria on selective Campylobacter agar.

A total of 67 oxidase-positive, gram-negative bacteria were tested for growth on selective Campylobacter agar (Blaser formulation, BBL Microbiology Systems, Cockeysville, Md.) at 42 degrees C under microaerophilic conditions. Although the growth of most of these bacteria was prevented, all strains of Achromobacter xylosoxidans, Pseudomonas aeruginosa, Pseudomonas putrefaciens, Pseudomonas alcaligenes, and Pseudomonas pseudoalcaligenes grew as well as Campylobacter fetus subsp. jejuni.

Alcaligenes↗
PubMed1983

Examination of the morphology of bacteria adhering to peritoneal dialysis catheters by scanning and transmission electron microscopy.

We examined Tenckhoff peritoneal catheters by scanning and transmission electron microscopy to study the morphology of bacterial adherence. Two catheters were removed from uninfected patients, three from patients with exit site infections, four from patients with peritonitis, and one from a patient with both exit site infection and peritonitis. Infecting organisms included three of Staphylococcus aureus and one each of Enterobacter sp., Staphylococcus epidermidis, Achromobacter xylosoxidans, Serratia sp., Klebsiella sp., and Candida albicans. Considerable morphological variation in adherence to the peritoneal dialysis apparatus occurred. No inflammatory cells were ever seen in association with infected cuffs, only two of the five patients with peritonitis had inflammatory cells associated with their catheters. In both instances, these cells tended to occur in clumps and demonstrated no flattening when in contact with the surface. Colonization of the catheter was uneven--bacteria tended to occur in clusters. Extensive matrix formation was evident in several instances, and condensation of this matrix onto the bacteria during the dehydration process rendered clumps of bacterial cells amorphous at times. Bacteria were adherent to the subcutaneous cuff in those patients with exit site infections. Gram-negative bacteria attached to individual dacron fibers of the cuff, often several layers deep. Gram-positive bacteria tended to adhere in clusters.

Bacteria↗
PubMed1984

Evaluation of the rapid NFT system for identification of gram-negative, nonfermenting rods.

This study evaluated the ability of the Rapid NFT system (API System SA, Montalieu-Vercieu, France) to accurately identify 262 clinically isolated, gram-negative, nonfermentative rods without additional tests. Identifications were classified as correct; low discrimination, with a spectrum of two or more possibilities (additional tests necessary for accurate identification); and incorrect. Correct identification rates were analyzed in two categories: (i) correct to species or biotype for all organism groups except Alcaligenes faecalis-odorans, Moraxella, Pseudomonas testosteroni-alcaligenes-pseudoalcaligenes, and Acinetobacter calcoaceticus biotype haemolyticus-alcaligenes (in this category, the latter four genus-biotype group identifications were taken as correct) and (ii) correct to species or biotype in all cases, including the above four groups. In category i, 87.4% of the strains were correctly identified, with 4.2% low discrimination and 8.4% incorrect. When the criteria of category ii were used, 71.8% of the strains were correctly identified, with 19.9% low discrimination. The Rapid NFT system provided excellent species identification of Pseudomonas and Flavobacterium spp., Bordetella bronchiseptica, and Achromobacter xylosoxidans strains. Within Acinetobacter calcoaceticus, differentiation between biotypes anitratus and lwoffi was satisfactory, but the system did not differentiate between biotypes haemolyticus and alcaligenes. Species resolution within the genera Moraxella and Alcaligenes was incomplete. All Alcaligenes faecalis strains were misidentified and accounted for 50% of misidentifications with the Rapid NFT system; however, these results may reflect taxonomic differences rather than true misidentifications. The Rapid NFT system is easy to inoculate and interpret and represents a worthwhile advance in the identification of gram-negative, nonfermentative rods.

Bacteria↗
PubMed1988

Evaluation of 9-chloro-9-[4-(diethylamino)phenyl]- 9,10-dihydro-10-phenylacridine hydrochloride (C-390) in broth and agar media for identification of Pseudomonas aeruginosa.

Brain heart infusion broth and Mueller-Hinton agar containing the compound 9-chloro-9-[4-(diethylamino)phenyl]- 9,10-dihydro-10-phenylacridine hydrochloride (C-390) were evaluated as selective media for identifying Pseudomonas aeruginosa. Of the 192 Pseudomonas spp. and 68 additional oxidase-positive or glucose-nonfermenting gram-negative organisms tested, only P. aeruginosa (120 of 121 isolates) and certain strains of Pseudomonas cepacia, Aeromonas hydrophila, and Achromobacter xylosoxidans were able to grow in brain heart infusion broth containing 15 micrograms of C-390 per ml. When production of green or yellow-green pigment after overnight growth on Mueller-Hinton agar containing 30 micrograms of C-390 per ml was used as the criterion for identification, only P. aeruginosa produced a positive test (96% sensitivity and 100% specificity). The agar medium, therefore, can provide a single differential medium for the overnight identification of P. aeruginosa.

Acridines↗
PubMed1989

Application of gas-liquid chromatography to the routine identification of nonfermenting gram-negative bacteria in clinical specimens.

A total of 430 strains of glucose-nonfermenting gram-negative bacteria representing 35 species were analyzed for their cellular fatty acid composition by gas-liquid chromatography (GLC). On the basis of qualitative differences in their cellular fatty acid composition, these bacteria could be divided into 19 distinct chromatographic groups. Eight Pseudomonas species, Achromobacter xylosoxidans, group Vd, and Agrobacterium radiobacter were identified from their fatty acid compositions alone. The other glucose-nonfermenting gram-negative bacterial species studied here, classified within nine distinct GLC groups, were easily recognized by using the GLC fatty acid analysis supplemented with a limited number of conventional biochemical tests. The results support the hypothesis that bacterial fatty acid composition is rather specific and that qualitative GLC fatty acid analysis can be adapted in the clinical laboratory either to provide additional criteria for differentiation of closely related groups or to serve as a rapid and highly reproducible method for their routine identification.

Acinetobacter↗
PubMed2002

Comparison of two culture methods for detection of tobramycin-resistant gram-negative organisms in the sputum of patients with cystic fibrosis.

A culture method utilizing quantitative plating on antibiotic-containing media has been proposed as a technique for the detection of tobramycin-resistant organisms that is more sensitive than standard methods. Typical sputum culture methods quantitate the relative amounts of each distinct morphotype, followed by antibiotic susceptibility testing of a single colony of each morphotype. Sputum specimens from 240 cystic fibrosis patients were homogenized, serially diluted, and processed in parallel by the standard method (MacConkey agar and OF basal medium with agar, polymyxin, bacitracin, and lactose) and by plating on antibiotic-containing media (MacConkey agar with tobramycin added at 25 microg/ml [MAC-25] and 100 microg/ml [MAC-100]). MICs of tobramycin were determined for all Pseudomonas aeruginosa isolates by broth microdilution. Growth of P. aeruginosa on MAC-25 was considered to be equivalent to a tobramycin MIC of > or = 16 microg/ml, and growth on MAC-100 was considered to be equivalent to a tobramycin MIC of > or = 128 microg/ml. Analysis of method-specific detection rates showed that tobramycin-containing medium was more sensitive than the standard method for the detection of tobramycin-resistant P. aeruginosa, Stenotrophomonas maltophilia, and Achromobacter xylosoxidans but was less sensitive for the detection of Burkholderia cepacia than the standard method. When MICs for P. aeruginosa that grew on tobramycin-containing medium were tested by broth microdilution, the MICs for 28 of 121 strains (23%) growing on MAC-25 and 22 of 56 strains (39%) growing on MAC-100 were MICs < 16 and < 128 microg/ml, respectively. Addition of a tobramycin-containing MacConkey plate to the routine media for sputum culture may provide additional, clinically relevant microbiologic data.

Adolescent↗
PubMed2002

Use of 16S rRNA gene sequencing for identification of nonfermenting gram-negative bacilli recovered from patients attending a single cystic fibrosis center.

During 1999, we used partial 16S rRNA gene sequencing for the prospective identification of atypical nonfermenting gram-negative bacilli isolated from patients attending our cystic fibrosis center. Of 1,093 isolates of nonfermenting gram-negative bacilli recovered from 148 patients, 46 (4.2%) gave problematic results with conventional phenotypic tests. These 46 isolates were genotypically identified as Pseudomonas aeruginosa (19 isolates, 12 patients), Achromobacter xylosoxidans (10 isolates, 8 patients), Stenotrophomonas maltophilia (9 isolates, 9 patients), Burkholderia cepacia genomovar I/III (3 isolates, 3 patients), Burkholderia vietnamiensis (1 isolate), Burkholderia gladioli (1 isolate), and Ralstonia mannitolilytica (3 isolates, 2 patients), a recently recognized species.

Alcaligenes↗
PubMed2002

Nosocomial infections caused by multidrug-resistant isolates of pseudomonas putida producing VIM-1 metallo-beta-lactamase.

Successful carbapenem-based chemotherapy for the treatment of Pseudomonas infections has been seriously hindered by the recent appearance of IMP- and VIM-type metallo-beta-lactamases, which confer high-level resistance to carbapenems and most other beta-lactams. Recently, multidrug-resistant Pseudomonas putida isolates for which carbapenem MICs were >/=32 micro g/ml were recovered from cultures of urine from three inpatients in the general intensive care unit of the Ospedale di Circolo, Varese, Italy. Enzyme assays revealed production of a metallo-beta-lactamase activity, while molecular analysis detected in each isolate a bla(VIM-1) determinant carried by an apparently identical medium-sized plasmid. Conjugation experiments were unsuccessful in transferring the beta-lactamase determinant to Escherichia coli or Pseudomonas aeruginosa. Macrorestriction analysis by pulsed-field gel electrophoresis demonstrated that the isolates were of clonal origin. PCR mapping and sequencing of the variable region of the plasmid-borne class 1 integron carrying the bla(VIM-1) determinant (named In110) showed that the bla(VIM-1)-containing cassette was identical to that previously found in strains of different species from other Italian hospitals and that the cassette array of In110 was not identical but clearly related to that of In70 (a bla(VIM-1)-containing plasmid-borne integron from an Achromobacter xylosoxidans isolate), pointing to a common origin of this cassette and to a related evolutionary history of their cognate integrons.

Aged↗
PubMed2002

Comparative evaluation of the BD Phoenix and VITEK 2 automated instruments for identification of isolates of the Burkholderia cepacia complex.

We evaluated two new automated identification systems, the BD Phoenix (Becton Dickinson) and the VITEK 2 (bioMérieux), for identification of isolates of the Burkholderia cepacia complex (BCC). The test sample included 42 isolates of the highly virulent and epidemic genomovar III, 45 isolates of B. multivorans, and 47 isolates of other members of the BCC. Rates of correct identification by the BD Phoenix and VITEK 2 were similar when all BCC isolates were considered (50 and 53%, respectively) but differed markedly for genomovar III (71 and 38%; P < 0.01) and for B. multivorans (58 and 89%; P < 0.001). For the BD Phoenix as well as the VITEK 2, taking all 134 isolates of the BCC together, rates of correct identification of clinical isolates (56 and 55%, respectively; n = 85) were higher than those of environmental isolates (21 and 39%, respectively; n = 28). Clinical isolates of genomovar III (n = 27) showed correct identification rates of 81% (BD Phoenix) and 48% (VITEK 2) (P < 0.01). Rates of misidentification for BD Phoenix and VITEK 2 were 9 and 17% for genomovar III, 22 and 7% for B. multivorans, and 36 and 13% for the other BCC members (P < 0.01), respectively. More than half of the isolates misidentified by each instrument were identified as Ralstonia pickettii, Ralstonia paucula (CDC IV C-2 group), Alcaligenes faecalis, Achromobacter spp., or, for the VITEK 2, "various nonfermenters." This study reemphasizes that confirmatory identification of BCC, preferably by molecular methods, is highly recommended.

Automation↗
PubMed2002

Prevalent bacterial species and novel phylotypes in advanced noma lesions.

The purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16S ribosomal DNA bacterial genes from DNA isolated from advanced noma lesions of four Nigerian children were PCR amplified with universally conserved primers and spirochetal selective primers and cloned into Escherichia coli. Partial 16S rRNA sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or closest relatives by comparison with sequences of known species or phylotypes. Nearly complete sequences of approximately 1,500 bases were obtained for most of the potentially novel species. A total of 67 bacterial species or phylotypes were detected, 25 of which have not yet been grown in vitro. Nineteen of the species or phylotypes, including Propionibacterium acnes, Staphylococcus spp., and the opportunistic pathogens Stenotrophomonas maltophilia and Ochrobactrum anthropi were detected in more than one subject. Other known species that were detected included Achromobacter spp., Afipia spp., Brevundimonas diminuta, Capnocytophaga spp., Cardiobacterium sp., Eikenella corrodens, Fusobacterium spp., Gemella haemoylsans, and Neisseria spp. Phylotypes that were unique to noma infections included those in the genera Eubacterium, Flavobacterium, Kocuria, Microbacterium, and Porphyromonas and the related Streptococcus salivarius and genera Sphingomonas and TREPONEMA: Since advanced noma lesions are infections open to the environment, it was not surprising to detect species not commonly associated with the oral cavity, e.g., from soil. Several species previously implicated as putative pathogens of noma, such as spirochetes and Fusobacterium spp., were detected in at least one subject. However, due to the limited number of available noma subjects, it was not possible at this time to associate specific species with the disease.

Adolescent↗
PubMed1998

Bombyx mori nucleopolyhedrovirus encodes a DNA-binding protein capable of destabilizing duplex DNA.

A DNA-binding protein (designated DBP) with an apparent molecular mass of 38 kDa was purified to homogeneity from BmN cells (derived from Bombyx mori) infected with the B. mori nucleopolyhedrovirus (BmNPV). Six peptides obtained after digestion of the isolated protein with Achromobacter protease I were partially or completely sequenced. The determined amino acid sequences indicated that DBP was encoded by an open reading frame (ORF16) located at nucleotides (nt) 16189 to 17139 in the BmNPV genome (GenBank accession no. L33180). This ORF (designated dbp) is a homolog of Autographa californica multicapsid NPV ORF25, whose product has not been identified. BmNPV DBP is predicted to contain 317 amino acids (calculated molecular mass of 36.7 kDa) and to have an isoelectric point of 7.8. DBP showed a tendency to multimerization in the course of purification and was found to bind preferentially to single-stranded DNA. When bound to oligonucleotides, DBP protected them from hydrolysis by phage T4 DNA polymerase-associated 3'-->5' exonuclease. The sizes of the protected fragments indicated that a binding site size for DBP is about 30 nt per protein monomer. DBP, but not BmNPV LEF-3, was capable of unwinding partial DNA duplexes in an in vitro system. This helix-destabilizing ability is consistent with the prediction that DBP functions as a single-stranded DNA binding protein in virus replication.

Amino Acid Sequence↗