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PubMed2000

Genomic and phenomic differentiation of Rhodococcus equi and related strains.

16S rDNA sequence and pyrolysis mass spectrometric analyses were carried out on representatives of Rhodococcus equi and marker strains of genera that encompass mycolic acid containing actinomycetes. The R. equi strains formed a monophyletic clade within the evolutionary radiation occupied by members of the genera Nocardia and Rhodococcus. The 16S rDNA sequence data also showed R. equi to be an heterogeneous taxon. This heterogeneity was underscored by the pyrolysis mass spectrometric data. These observations are in line with those of previous studies where similar profiles of relatedness were found between pyrolysis mass spectral data and the results of DNA:DNA pairing and numerical phenetic studies.

Actinomycetales↗

PubMed2001

Heterobactins: A new class of siderophores from Rhodococcus erythropolis IGTS8 containing both hydroxamate and catecholate donor groups.

We report here on a new class of siderophores isolated from Rhodococcus erythropolis IGTS8, the first structurally characterized from any species of Rhodococcus and for which we suggest the name heterobactins. These siderophores consist of a tripeptide of sequence (N-OH)-L-Orn-Gly-D-Orn-(delta-N-dihydroyxbenzoate). The alpha amino group of the D-Orn is derivatized either as a 2-hydroxybenzoxazolate in heterobactin A or remains free in heterobactin B. The structures were determined by a combination of amino acid analysis, mass spectrometry and NMR methods. The two new compounds are true siderophores in that they relieve iron limited growth in the producing strain. The heterobactins are also transported by other non-producing bacteria. Growth promotion tests using various transport mutants revealed that in E. coli heterobactin A is only recognized by the catecholate receptor Cir while heterobactin B is taken up in both E.coli and A. flavescens JG9 via a hydroxamate transport system.

Bacterial Proteins↗

PubMed2001

Detection of antibodies against Rhodococcus equi in Alpaca (Lama pacos) in Italy.

After isolating the two virulent strains of Rhodococcus equi from Alpaca, a serological survey of Rhodococcus equi infection was carried out on 57 blood samples of Alpaca collected in Central Italy. The survey was performed with an ELISA test using a reference R. equi strain as antigen (ATCC 33701). Four (7.0%) sera (OD greater or equal to 0.3) tested positive, while five (8.77%) were considered doubtful (OD between 0.2 and 0.3). This is the first serological survey of R. equi infection in Alpaca in Italy. The results indicate that besides the horse R. equi infection could also affect some ruminant species. The ELISA test was recently introduced as a reliable diagnostic method in horses and was adapted to alpaca.

Actinomycetales Infections↗

PubMed2004

Rapid determination of vapA/vapB genotype in Rhodococcus equi using a differential polymerase chain reaction method.

Rhodococcus equi is a facultative pathogen of foals. Infection causes an often fatal pulmonary pneumonia. The organism has also been isolated from pigs, cattle, humans and the environment. Equine virulence has a high positive correlation with the expression of a 17.4 kD polypeptide of unknown function, VapA, the product of the plasmid-encoded vapA gene. More recently an isogene of vapA, referred to as vapB and encoding an 18.2 kDa polypeptide, has been identified among pig and human isolates. The two genes share > 80% sequence identity, yet their host strains apparently exhibit different pathogenicity profiles (for example by reference to virulence in mouse model system and host specificity). In this study, a polymerase chain reaction (PCR) technique was developed that permits the selective amplification of vapA and vapB. Using this technique the distribution of the two genes among 35 randomly selected isolates of Rhodococcus equi from various animal and environmental sources was determined. Using this technique the genotype of each isolate could be unambiguously assigned as vapA+, vapB+ or vap- (i.e., scoring negative for both vapA and vapB). No isolate scored positive for both vapA and vapB. 100% of equine isolates scored vapA+, confirming the status of vapA as a reliable marker of equine virulence. All three genotypes were found among human isolates; porcine isolates scored either vapB+ or vap- and no vapA+ isolates were present in this sample. Rigorous statistical analysis using the Fisher Exact test confirmed that the high frequency of vapA+ among equine isolates is significant; however the sample size was too small to draw statistically significant conclusions regarding the distribution of genotypes among within other animal groups.

Actinomycetales Infections↗

PubMed2002

Rhodococcus equi infection in transplant recipients: a case of mistaken identity and review of the literature.

The incidence of Rhodococcus equi infection in solid-organ transplant recipients continues to rise throughout the world. Unfortunately, this opportunistic pathogen is still underestimated and potentially disregarded by physicians and microbiology laboratories due to its morphology on Gram staining. Pulmonary involvement is the most common finding in the immunocompromised host. We report a case of a 63-year-old heart-transplant recipient who presented with increasing fatigue and nonproductive cough for 3 weeks. After full evaluation, a lung abscess was demonstrated by thoracic computerized tomography (CT). Blood and sputum cultures were remarkable for heavy "diphtheroids." Although the Gram-stain result was initially interpreted as a contaminant, a clinical suspicion for Rhodococcus assisted in further investigation. Broncheoalveolar lavage and CT-guided biopsy of the lung abscess revealed heavy growth of diphtheroids. However, further evaluation by a reference laboratory demonstrated mycolic acid staining consistent with R. equi. Surgical drainage and prolonged antibiotic therapy resulted in complete remission of the pneumonia and abscess. This represents the fourth reported case of R. equi infection in a heart transplant recipient. It is imperative that all physicians and laboratory staff consider R. equi when an immunocompromised patient has any type of pneumonia, especially with abscess formation.

Actinomycetales Infections↗

PubMed2026

Rhodococcus folensis sp. nov., an orange-red-pigmented bacterium from mining soil.

Mining-impacted environments represent chemically complex ecosystems that may harbor metabolically versatile and pigment-producing microorganisms. During a survey of pigment-producing bacteria from abandoned mining soil in Trabzon, Türkiye, a red-pigmented strain, designated FMA22T, was isolated and characterized using a polyphasic taxonomic approach. 16 S rRNA gene sequence analysis placed the strain within the genus Rhodococcus, showing the highest similarity to R. corynebacterioides DSM 20,151T (99.57%), R. kroppenstedtii DSM 44908ᵀ (99.06%) and R. trifolii T8T (98.96%). The strain was Gram-stain-positive, aerobic and non-motile, and grew at 4-40 °C. Polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylcholine, five unidentified glycolipids, four unidentified lipids, one unidentified phospholipid and one unidentified phosphoglycolipid; MK-8(H2) was the major respiratory quinone. Major fatty acids were C18:1 ω9c, summed feature 3 (C16:1 ω7c/C16:1 ω6c) and C16:0. ANI and dDDH values with the closest relatives were below 76.8% and 20.5%, respectively. The draft genome (4.23 Mb; 67.2 mol% G + C; 4,106 CDSs) harbors a terpene-associated carotenoid cluster containing crtB, crtI and crtY. The orange-red pigment (λmax = 475 nm) showed antioxidant activity (DPPH SC₅₀ = 5.38 mg mL⁻¹; FRAP = 4.34 µmol TE g⁻¹) and weak but measurable HIV-1 reverse transcriptase inhibition (IC₅₀ = 22 mg mL⁻¹). These data support the proposal of Rhodococcus folensis sp. nov., with FMA22ᵀ (= LMG 34144ᵀ = DSM 120048ᵀ) as the type strain.

Soil Microbiology↗

PubMed2002

Cell surface hydrophobicity and mycolic acid composition of Rhodococcus strains isolated from activated sludge foam.

The bacteria causing foaming in activated sludge plants are considered to be hydrophobic, and their hydrophobicity is assumed to be a crucial factor in their foam-forming ability. This study showed no consistent relationship between cell surface hydrophobicity (CSH), as determined by microbial adherence to hydrocarbons, of three Rhodococcus spp. isolated from activated sludge foam and their ability to produce a stable foam. There also appeared to be no correlation between the mycolic acid composition of these strains, in terms of chain length or degree of unsaturation, and either CSH or foaming ability. Zeolite and bentonite successfully prevented foaming by a Rhodococcus sp. in pure culture, which suggests that cell surface charge may also play a role in foam stabilisation.

Bacterial Adhesion↗

PubMed2006

Constitutive expression of catABC genes in the aniline-assimilating bacterium Rhodococcus species AN-22: production, purification, characterization and gene analysis of CatA, CatB and CatC.

The aniline-assimilating bacterium Rhodococcus sp. AN-22 was found to constitutively synthesize CatB (cis,cis-muconate cycloisomerase) and CatC (muconolactone isomerase) in its cells growing on non-aromatic substrates, in addition to the previously reported CatA (catechol 1,2-dioxygenase). The bacterium maintained the specific activity of the three enzymes at an almost equal level during cultivation on succinate. CatB and CatC were purified to homogeneity and characterized. CatB was a monomer with a molecular mass of 44 kDa. The enzyme was activated by Mn2+, Co2+ and Mg2+. Native CatC was a homo-octamer with a molecular mass of 100 kDa. The enzyme was stable between pH 7.0 and 10.5 and was resistant to heating up to 90 degrees C. Genes coding for CatA, CatB and CatC were cloned and named catA, catB and catC respectively. The catABC genes were transcribed as one operon. The deduced amino acid sequences of CatA, CatB and CatC showed high identities with those from other Gram-positive micro-organisms. A regulator gene such as catR encoding a regulatory protein was not observed around the cat gene cluster of Rhodococcus sp. AN-22, but a possible relic of catR was found in the upstream region of catA. Reverse transcriptase-PCR and primer extension analyses showed that the transcriptional start site of the cat gene cluster was located 891 bp upstream of the catA initiation codon in the AN-22 strain growing on both aniline and succinate. Based on these data, we concluded that the bacterium constitutively transcribed the catABC genes and translated its mRNA into CatA, CatB and CatC.

Aniline Compounds↗

PubMed1998

Purification and characterization of catechol 1,2-dioxygenase from Rhodococcus rhodochrous NCIMB 13259 and cloning and sequencing of its catA gene.

A method was developed for the purification of catechol 1, 2-dioxygenase from Rhodococcus rhodochrous NCIMB 13259 that had been grown in the presence of benzyl alcohol. The enzyme has very similar apparent Km (1-2 microM) and Vmax (13-19 units/mg of protein) values for the intradiol cleavage of catechol, 3-methylcatechol and 4-methylcatechol and it is optimally active at pH9. Cross-linking studies indicate that the enzyme is a homodimer. It contains 0.6 atoms of Fe per subunit. The enzyme was crystallized with 15% (w/v) poly(ethylene glycol) 4000/0.33 M CaCl2/25 mM Tris (pH7.5) by using a microseeding technique. Preliminary X-ray characterization showed that the crystals are in space group C2 with unit-cell dimensions a=111.9 A, b=78.1 A, c=134.6 A, beta=100 degrees. An oligonucleotide probe, made by hemi-nested PCR, was used to clone the gene encoding catechol 1,2-dioxygenase (catA). The deduced 282-residue sequence corresponds to a protein of molecular mass 31539 Da, close to the molecular mass of 31558 Da obtained by electrospray MS of the purified enzyme. catA was subcloned into the expression vector pTB361, allowing the production of catechol 1,2-dioxygenase to approx. 40% of the total cellular protein. The deduced amino acid sequence of the enzyme has 56% and 75% identity with the catechol 1, 2-dioxygenases of Arthrobacter mA3 and Rhodococcus erythropolis AN-13 respectively, but less than 35% identity with intradiol catechol and chlorocatechol dioxygenases of Gram-negative bacteria.

Amino Acid Sequence↗

PubMed1999

Identification and environmental detection of Rhodococcus species by 16S rDNA-targeted PCR.

Bacteria of the genus Rhodococcus can degrade a wide range of organic pollutants and catalyse many useful biotransformations. There is a need for improved tests to identify Rhodococcus species. PCR-based methods for species identification offer advantages in terms of speed and accuracy over traditional methods and can allow direct detection of microbes in environmental samples., PCR tests, using primers targeted at species-specific sequences in the 16S rRNA gene, were successfully developed for R. globerulus, R. erythropolis, R. opacus and R. ruber. These tests gave positive results with all or most strains of target species but did not generally cross-react with other species. Cases of apparent cross-reaction were shown to be due to prior misclassification of strains of R. opacus as R. erythropolis and of strains of R. ruber as R. rhodochrous. A simple and rapid method for the extraction and purification of DNA from soil was developed and successfully applied to the PCR detection of indigenous R. erythropolis in an environmental sample. Cell lysis in the samples was achieved by lysozyme and sarkosyl treatment, aided by freeze-thaw cycles. Removal of humic compounds inhibitory to PCR was accomplished by CTAB treatment with solvent extraction and, if necessary, passage of extracts through Sepharose CL-6B in a spun-column format. Extracts prepared using a tris-EDTA buffer were much clearer than those prepared using a sodium phosphate buffer, indicating lower levels of humic compounds. A detection limit of 104 cfu g-1 of soil was achieved and the use of a secondary PCR allowed detection of 1 cfu g-1.

Bacterial Typing Techniques↗

PubMed1999

Expression of a functional antibody fragment in the gut of Rhodnius prolixus via transgenic bacterial symbiont Rhodococcus rhodnii.

Expression within insects of foreign antiparasitic gene products via microbial symbionts could be used to prevent transmission of vector-borne pathogens to vertebrate hosts. Genetically transformed symbiotic bacteria Rhodococcus rhodnii expressed functional antibody fragments (rDB3 encoding murine V(H)/K which binds progesterone) that were exported into the gut lumen of the triatomine bug Rhodnius prolixus (Hemiptera: Reduviidae), a vector of Chagas disease. Transgenic symbionts were maintained in successive nymphal instars and adults of Rhodnius prolixus despite competition with native untransformed Rhodococcus rhodnii. This is the first description of a functional mammalian antibody fragment expressed in an insect. Our system is a model for constructing paratransgenic insects (insects carrying transformed symbionts) with compromised ability to transmit pathogens.

Animals↗

PubMed2003

Cloning of Baeyer-Villiger monooxygenases from Comamonas, Xanthobacter and Rhodococcus using polymerase chain reaction with highly degenerate primers.

To clone novel type 1 Baeyer-Villiger monooxygenase (BVMO) genes, we isolated or collected 25 bacterial strains able to grow on alicyclic compounds. Twelve of the bacterial strains yielded polymerase chain reaction (PCR) fragments with highly degenerate primers based on the sequences of known and putative BVMOs. All these fragments were found to encode peptides homologous to published BVMO sequences. The complete BVMO genes and flanking DNA were cloned from a Comamonas, a Xanthobacter and a Rhodococcus strain using the PCR fragments as probes. BVMO genes cloned from the first two strains could be expressed to high levels in Escherichia coli using standard expression vectors, and the recombinants converted cyclopentanone and cyclohexanone to the corresponding lactones. The Rhodococcus BVMO, a putative steroid monooxygenase, could be expressed after modification of the N-terminal sequence. However, recombinants expressing this protein did not show activity towards progesterone. An esterase homologue located directly upstream of the Xanthobacter BVMO gene and a dehydrogenase homologue encoded directly downstream of the Comamonas sp. NCIMB 9872 BVMO gene were also expressed in E. coli and shown to specify lactone hydrolase and cyclohexanol dehydrogenase activity respectively.

Amino Acid Sequence↗

PubMed1996

Characterization of the gene cluster of high-molecular-mass nitrile hydratase (H-NHase) induced by its reaction product in Rhodococcus rhodochrous J1.

The 4.6-kb region 5'-upstream from the gene encoding a cobalt-containing and amide-induced high molecular mass-nitrile hydratase (H-NHase) from Rhodococcus rhodochrous J1 was found to be required for the expression of the H-NHase gene with a host-vector system in a Rhodococcus strain. Sequence analysis has revealed that there are at least five open reading frames (H-ORF1 approximately 5) in addition to H-NHase alpha- and beta-subunit genes. Deletion of H-ORF1 and H-ORF2 resulted in decrease of NHase activity, suggesting a positive regulatory role of both ORFs in the expression of the H-NHase gene. H-ORF1 showed significant similarity to a regulatory protein, AmiC, which is involved in regulation of amidase expression by binding an inducer amide in Pseudomonas aeruginosa. H-ORF4, which has been found to be uninvolved in regulation of H-NHase expression by enzyme assay for its deletion transformant and Northern blot analysis for R. rhodochrous J1, showed high similarity to transposases from insertion sequences of several bacteria. Determination of H-NHase activity and H-NHase mRNA levels in R. rhodochrous J1 has indicated that the expression of the H-NHase gene is regulated by an amide at the transcriptional level. These findings suggest the participation of H-ORF4 (IS1164) in the organization of the H-NHase gene cluster and the involvement of H-ORF1 in unusual induction mechanism, in which H-NHase is formed by amides (the products in the NHase reaction), but not by nitriles (the substrates).

Amino Acid Sequence↗

PubMed1997

Structure of the photoreactive iron center of the nitrile hydratase from Rhodococcus sp. N-771. Evidence of a novel post-translational modification in the cysteine ligand.

Nitrile hydratase (NHase) from Rhodococcus sp. N-771 is a photoreactive enzyme that is inactivated by nitrosylation of the non-heme iron center and activated by photodissociation of nitric oxide (NO). To obtain structural information on the iron center, we isolated peptide complexes containing the iron center by proteolysis. When the tryptic digest of the alpha subunit isolated from the inactive form was analyzed by reversed-phase high performance liquid chromatography, the absorbance characteristic of the nitrosylated iron center was observed in the peptide fragment, Asn105-Val-Ile-Val-Cys-Ser-Leu-Cys-Ser-Cys-Thr-Ala-Trp-Pro-Ile-Leu - Gly-Leu-Pro-Pro-Thr-Trp-Tyr-Lys128. The peptide contained 0.79 mol of iron/mol of molecule as well as endogenous NO. Subsequently, by digesting the peptide with thermolysin, carboxypeptidase Y, and leucine aminopeptidase M, we found that the minimum peptide segment required for the nitrosylated iron center is the 11 amino acid residues from alphaIle107 to alphaTrp117. Furthermore, by using mass spectrometry, protein sequence, and amino acid composition analyses, we have shown that the 112th Cys residue of the alpha subunit is post-translationally oxidized to a cysteine-sulfinic acid (Cys-SO2H) in the NHase. These results indicate that the NHase from Rhodococcus sp. N-771 has a novel non-heme iron enzyme containing a cysteine-sulfinic acid in the iron center. Possible ligand residues of the iron center are discussed.

Amino Acid Sequence↗

PubMed1996

Rhodococcus equi infection in 3 AIDS patients.

Three cases of AIDS complicated by Rhodococcus equi infection are reported. At least one of the patients acquired his Rhodococcus infection in Africa. Despite the fact that the R. equi strains were susceptible to tetracycline, erythromycin, amikacin, co-trimoxazole, rifampicin and vancomycin, these antibiotics were clinically not successful. A clinical improvement was observed in only one patient during teicoplanin and imipenem-cilastatin treatment. Multicentre clinical trials are needed to determine the optimal treatment of R. equi infections in AIDS patients.

AIDS-Related Opportunistic Infections↗

PubMed2000

Cloning and expression of gene encoding a novel endoglycoceramidase of Rhodococcus sp. strain C9.

Endoglycoceramidase (EGCase) is an enzyme capable of cleaving the glycosidic linkage between oligosaccharides and ceramides of various glycosphingolipids. We previously reported that the Asn-Glu-Pro (NEP) sequence is part of the active site of EGCase of Rhodococcus sp. strain M-777. This paper describes the molecular cloning of a new EGCase gene utilizing the NEP sequence from the genomic library of Rhodococcus sp. strain C9, which was clearly distinguishable from M-777 by 16S rDNA analysis. C9 EGCase possessed an open reading frame of 1,446 bp encoding 482 amino acids, and showed 78% and 76% identity to M-777 EGCase II at the nucleotide and amino acid levels, respectively. Interestingly, C9 EGCase showed the different specificity to the M-777 enzyme: it hydrolyzed b-series gangliotetraosylceramides more slowly than the M-777 enzyme, whereas both enzymes hydrolyzed a-series gangliosides and neutral glycosphingolipids to the same extent.

Amino Acid Sequence↗

PubMed1992

Case report: Rhodococcus equi pneumonia in a patient infected by the human immunodeficiency virus.

Rhodococcus equi, a facultative intracellular bacterium, is a common cause of pulmonary infection in farm animals, especially foals. Pulmonary and disseminated infection caused by this organism is occasionally seen in humans, especially in patients whose cell-mediated immunity has been altered by glucocorticoids or cytotoxic chemotherapy. Not surprisingly, the organism may cause serious disease in human immunodeficiency virus (HIV)-infected humans whose T cell-dependent immune system has been profoundly suppressed. This report describes an HIV infected patient with Rhodococcus equi pneumonia and reviews nine additional HIV-infected patients. Treatment in humans is not standardized. Studies in foals indicate that erythromycin and rifampin together are the treatment of choice. The patient in this report responded to this treatment briefly before relapsing and dying of the infection.

Actinomycetales Infections↗

PubMed1996

Rhodococcus percolatus sp. nov., a bacterium degrading 2,4,6-trichlorophenol.

A bacterial strain that was able to mineralize 2,4,6-trichlorophenol was isolated from a chlorophenol-fed percolator and was identified as a member of the genus Rhodococcus on the basis of chemotaxonomic characteristics and 16S RNA phylogenetic inference data. This organism (strain MBS1T [T = type strain]) exhibited a typical irregular rod-coccus cycle, and the cells had fimbria-like structures on their surfaces. The diagnostic cell wall amino acid was meso-diaminopimelic acid, and the sugars were arabinose and galactose; the mycolic acids contained 46 to 54 carbon atoms. The main menaquinone was MK-8(H2), and MK-9(H2) was a minor component. The cellular phospholipids were phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside, phosphatidylglycerol, and diphosphatidylglycerol. Tuberculostearic acid was present. The whole-cell fatty acids were straight-chain acids with 14 to 18 C atoms. The G+C content of the DNA was 67.4 mol%. This organism grew on sucrose, pyruvate, and 2,4,6-trichlorophenol, and it oxidized a large number of carbon compounds, including catechol, 3-hydroxyphenylacetic acid, and phenol. It also exhibited beta-galactosidase, urease, and 2-acetyl-lactate decarboxylase activities. On a phylogenetic tree that was based on 16S ribosomal DNA gene sequences strain MBS1T was found among the rhodococci on an independent branch. On the basis of the chemotaxonomic and phenotypic characteristics of strain MBS1T and its phylogenetic position we suggest that this bacterium should be placed in a new species, Rhodococcus percolatus; the specific epithet was chosen because the organism was isolated by using an enriched percolator. The type strain is strain MBS1.

Base Sequence↗