Efficient biodegradation of di-(2-ethylhexyl) phthalate by a novel strain Nocardia asteroides LMB-7 isolated from electronic waste soil.

The di-2-ethylhexyl phthalate (DEHP) degrading strain LMB-7 was isolated from electronic waste soil. According to its biophysical/biochemical characteristics and 16S rRNA gene analysis, the strain was identified as Nocardia asteroides. Optimal pH and temperature for DEHP degradation were 8.0 and 30 °C, respectively, and DEHP removal reached 97.11% after cultivation for 24 h at an initial concentration of 400 mg/L. As degradation intermediates, di-butyl phthalates, mono-2-ethylhexyl phthalate and 2-ethylhexanol could be identified, and it could be confirmed that DEHP was completely degraded by strain LMB-7. To our knowledge, this is a new report of DEHP degradation by a strain of Nocardia asteroides, at rates higher than those reported to date. This finding provides a new way for DEHP elimination from environment.

The Complexities of Nocardia Taxonomy and Identification.

Nocardia species are a complex group of organisms considered to belong to the aerobic actinomycetes. Of the validly described species, many have been implicated as the cause of serious human infections, especially in immunocompromised patients. The genus has a complicated taxonomic history; this is especially true for Nocardia asteroides, the type species of the genus and previously the most frequently reported nocardial taxon from human specimens. We provide background on the current taxonomy of Nocardia, with a focus on clinically relevant species, and discuss the currently available methods used to accurately identify isolates to the species, complex, or group level.

Nocardia Arthritidis Keratitis: Case Report and Review of the Literature.

INTRODUCTION: Keratitis due to Nocardia infection is not commonly encountered in clinical practice and may therefore be mistaken for fungal or viral keratitis leading to delayed treatment and increased risk of permanent visual impairment. CASE: An otherwise healthy 27 years old Caucasian Active Duty military member presented to the clinic with three days of light sensitivity and irritation of his right eye. He carried a history of PRK in both eyes six years prior and admitted to recent contact lens overuse. With empiric treatment for typical bacterial keratitis including corticosteroids, his condition worsened on close follow-up. While awaiting cultures, a shift to fortified topical antibiotics tobramycin, moxifloxacin and ciprofloxacin showed improvement with closure of the epithelial defect. Ulcerative relapse occurred with withdrawal of therapy. Culture proven Nocardia arthritidis prompted successful treatment with topical antibiotic amikacin. On follow-up at three months, the patient was doing well with a small peripheral anterior stromal scar without permanent visual sequelae. Visual acuity returned to baseline of 20/20 in the affected eye. CONCLUSION: Keratitis caused by Nocardia species, including arthritidis, responds well to amikacin. Late diagnosis and early treatment withdrawal may lead to a prolonged recovery. Current literature indicates that corticosteroids may be harmful in the treatment of Nocardia keratitis. Increased awareness of Nocardia as an ocular pathogen has the potential to reduce unnecessary morbidity related to delayed diagnosis, inadequate therapy and inappropriate use of corticosteroids.

Lack of evidence for Nocardia asteroides in brain specimens from Lewy body-containing disorders.

Previous studies have suggested that Nocardia asteroides may play a role in the pathogenesis of Parkinson's disease (PD), including the production of Lewy bodies, the inclusion bodies present in this disorder. This study explored the possible connection between Nocardia and two Lewy body-containing disorders, PD and dementia with Lewy bodies (DLB). Substantia nigra specimens from individuals with PD, DLB, other neurodegenerative disorders, and normal subjects were evaluated for nocardial infection by in situ hybridization, PCR, and Gram staining. Brain specimens from a cynomolgus monkey experimentally infected with N. asteroides for 48 h served as the controls for in situ hybridization and Gram staining, and a nocardial pellet was the PCR control. The organism was detected by in situ hybridization and Gram stain in the experimentally infected monkey brain, and by PCR from the nocardial pellet. However, in situ hybridization reactivity was detected in only three of the 125 human brain specimens (2.4%; one case each of PD, DLB, and Alzheimer's disease), and none of the specimens was positive for Nocardia by PCR or Gram staining. These findings do not support an association of Nocardia with Lewy body-containing disorders.

Biochemical identification and molecular characterization (PCR-RFLP) of Nocardia isolates from sputum.

BACKGROUND: Nocardia identification has been based on biochemical and morphological characteristics. However, molecular biology techniques allow a better characterization of species and biotypes that are related to invasive diseases. METHODS: Twelve isolates of Nocardia spp. were obtained from sputum of patients with tuberculosis under retreatment. Identification was done based on morphological characteristics, biochemical tests (casein, tyrosine, xanthine, gelatin, and urea) and molecular biology techniques (PCR-RFLP) using restriction enzymes MspI, HinfI, BsaHI, HaeIII and BstEII. RESULTS: Biochemical tests identified the 12 isolates as Nocardia asteroides. PCR-RFLP technique identified nine isolates to species and biotype level: five as N. asteroides type II, two as N. asteroides type VI, and two as N. asteroides type I. The remaining three isolates were identified as follows: one to species level as N. farcinica and two at genus level as Nocardia sp. CONCLUSIONS: Significant statistical differences between the use of traditional techniques and PCR-RFLP were not found at genus level, but there were important differences at species and biotype level. Biochemical tests identified correctly the actinomycete isolates as belonging to Nocardia genus, but at N. asteroides complex level were not able to discern among their different species. PCR-RFLP is a rapid, non-expensive, and reliable method that allows to discriminate the N. asteroides complex species, identifying biotypes related to invasive disease. Our results suggest that the hospital environment was not a contamination source.

Comparison of PCR and culture for detection of Nocardia asteroides in brain specimens from experimentally infected BALB/c mice.

Systemic infection of BALB/c mice with Nocardia asteroides strain GUH-2 results in widespread replication of the organism in the brain, followed by its immune-mediated clearance. The present study compared the sensitivity of polymerase chain reaction (PCR) to bacterial culture for detection of cerebral nocardial infection in this experimental system. Mice (n=4/time point) were administered N. asteroides by intravenous injection, and brain specimens were evaluated for Nocardia by PCR and culture at post-infection days 2, 7, 14 and 21. Nocardia was detected by PCR in all infected animals on post-infection days 2, 7, and 14, and in one of four mice on post-infection day 21; in contrast, the organism was detected by culture only on post-infection days 2 and 7. These findings suggest that PCR may be more sensitive than culture for the detection of low numbers of Nocardia in the brain.

Rapid identification of Nocardia farcinica clinical isolates by a PCR assay targeting a 314-base-pair species-specific DNA fragment.

Nocardia farcinica is the most clinically significant species within the Nocardia asteroides complex. Differentiation of N. farcinica from other members of N. asteroides complex is important because this species characteristically demonstrates resistance to several extended-spectrum antimicrobial agents. Traditional phenotypic characterization of this species is time- and labor-intensive and often leads to misidentification in the clinical microbiology laboratory. We previously observed a 409-bp product for all strains of N. farcinica by using randomly amplified polymorphic DNA analysis with the primer DKU49. In this investigation, the 409-bp fragment was sequenced and then used to design a specific primer pair, Nf1 (16-mer) and Nf2 (16-mer), complementary to the 409-bp fragment. PCR amplification of genomic DNA from 28 N. farcinica isolates with Nf1 and Nf2 generated a single intense 314-bp fragment. The specificity of the assay with these primers was verified, since there were no PCR amplification products observed from heterologous nocardial species (n = 59) or other related bacterial genera (n = 41). Restriction enzyme digestion using CfoI and direct sequencing of the 314-bp fragment further confirmed the specificity of the assay for N. farcinica. This highly sensitive and specific PCR assay provides a rapid (within 1 day of obtaining DNA) method for identification of this medically important emerging pathogen. Rapid diagnosis of N. farcinica infection may allow for earlier initiation of effective therapy, thus improving patient outcome.

Characterization of Nocardia asteroides isolates from different ecological habitats on the basis of repetitive extragenic palindromic-PCR fingerprinting.

Thirteen isolates of Nocardia asteroides from both soils and aquatic samples (lake and moat sediments, as well as scum from activated sludge), together with a type strain and two known clinical isolates of this species, were characterized by repetitive extragenic palindromic-PCR fingerprinting with the BOX-A1R primer. The resulting DNA fingerprint patterns proved to be strain specific, and cluster analysis distinguished the soil isolates, the aquatic isolates, and the known strains as being in separate groups.

Chronic granulomatous pleuritis caused by nocardia: PCR based diagnosis by nocardial 16S rDNA in pathological specimens.

Nocardiosis is an uncommon infection caused by the aerobic actinomycete nocardia. Identification of the pathogen is essential for the definitive diagnosis and for an effective treatment. This report describes a case of chronic granulomatous pleuritis caused by nocardia. A 59 year old Japanese man had a history of repeated pyothorax. Right pleural decortication and thoracic drainage were performed. Microbiological examinations of the drained fluid failed to identify a pathogen. Pathological examinations revealed Gram positive filamentous and branching bacilli in the granulomatous lesion of the pleura. Sequencing of the 971 bp 16S ribosomal DNA extracted and amplified from paraffin wax embedded sections identified the microorganism as Nocardia sp. IFM 0860. The patient received sulfamethoxazol/trimethoprim and minocycline. Although the presence of a brain abscess was disclosed by systemic examination, the clinical course has been favourable. In this patient, polymerase chain reaction analysis of 16S ribosomal DNA in pathological specimens was useful in making an accurate diagnosis of nocardiosis and in determining the appropriate treatment.

Phylogeny of the genus Nocardia based on reassessed 16S rRNA gene sequences reveals underspeciation and division of strains classified as Nocardia asteroides into three established species and two unnamed taxons.

Conventional identification of Nocardia in the routine laboratory remains problematic due to a paucity of reliable phenotypic tests and due to the yet-unresolved taxonomy of strains classified as belonging to the species Nocardia asteroides, which comprises the type strain and isolates with drug pattern types II and VI. The 16S rRNA gene of 74 representative strains of the genus Nocardia, encompassing 25 established species, was sequenced in order to provide a molecular basis for accurate species identification and with the aim of reassessing the phylogeny of taxons assigned to the species N. asteroides. The result of this phylogenetic analysis confirms that the interspecies heterogeneity of closely related nocardial species can be considerably low (a sequence divergence of only 0.5% was found between N. paucivorans and N. brevicatena). We observed a sequence microheterogeneity (sequence divergence of fewer than five bases) in 8 of 11 species of which more than one strain in the species was studied. At least 10 taxons were found that merit description as new species. Strains previously classified as N. asteroides fell into five distinct phylogenetic groups: the type strain cluster (N. asteroides sensu strictu), N. abscessus, N. cyriacigeorgica, and two clusters closely related to N. carnea or N. flavorosea. The strains within the latter two groups probably represent new species, pending further genetic and phenotypic evaluation. Restricted phenotypic data revealed that N. abscessus, N. cyriacigeorgica, and the two Nocardia species taxons are equivalent to drug patterns I, VI, and II, respectively. In the future, these data will help in finding species-specific markers after adoption of a more precise nomenclature for isolates closely related to N. asteroides and unravel confusing phenotypic data obtained in the past for unresolved groups of strains that definitely belong to separate taxons from a phylogenetic point of view.

Molecular and biochemical analysis of AST-1, a class A beta-lactamase from Nocardia asteroides sensu stricto.

A beta-lactamase gene was cloned from a Nocardia asteroides sensu stricto clinical isolate. A recombinant plasmid, pAST-1, expressed the beta-lactamase AST-1 in Escherichia coli JM109. Its pI was 4.8, and its relative molecular mass was 31 kDa. E. coli JM109(pAST-1) was resistant to penicillins and narrow-spectrum cephalosporins. The beta-lactamase AST-1 had a restricted hydrolytic activity spectrum. Its activity was partially inhibited by clavulanic acid but not by sulbactam and tazobactam. AST-1 is an Ambler class A beta-lactamase sharing 65% amino acid identity with beta-lactamase FAR-1, the most closely related enzyme.

[Conjugational actinomycetes of plasmid RSF101 from Escherichia coli to the rare actinomyceces of Nocardia asteriodes and Streptoverticillum caespitosus].

RSF1010 is a naturally occurring Escherichia coli broad host-range plasmid about 8.7 kb in size. It can be mobilized at high frequency between different gram-negative bacterial species when transfer functions are available in trans. Following the pioneering work of conjugational transfer of RSF1010 from E. coli to Streptomyces lividans and Mycobacterium smegmatis, the transfer of this plasmid by conjugation from E. coli S17.1 tp two gram-positive rare actinomycetes, Nocardia asteroides 3927 and Streptoverticillum caespitosus ATCC27422 was first time reported in this study. Southern blot analysis of the total DNA extracted from the actinomycetes' exconjugants proved that RSF1010 had been transferred from E. coli into the two new hosts and maintained staby in the exconjugants. Meanwhile, partial deletions of RSF1010 replicon loosing its antibiotics resistance makers were readily detected in E. coli. The implenmentation of this observation was discussed.

Non-inducible, mainly cell-associated beta-lactamase from Nocardia asteroides strain 108.

The beta-lactamase of the soil-borne strain 108 (parental strain) of Nocardia asteroides is a non-inducible enzyme mainly associated with the cells; it can be efficiently extracted by ultrasonication and SDS treatment. Crude enzyme preparations showed penicillinase and cephalosporinase activity. The kinetics of beta-lactamase production and in-vitro susceptibility to combinations of beta-lactam antibiotics plus beta-lactamase inhibitors have been studied in two stable overproducer mutants (A14 and B1) obtained by mutagenization of the parental strain with nitrosoguanidine. The cell-associated enzyme increased with bacterial growth in parental and mutant strains and was particularly abundant in stationary phase cells. The beta-lactamase inhibitors sulbactam and clavulanic acid decreased MIC values of penicillins more efficiently in the parental strain than in mutants, thus indicating some involvement of the enzyme in the resistance of N. asteroides strain 108 to beta-lactam antibiotics.

Investigation of a pseudo-outbreak of Nocardia asteroides infection by pulsed-field gel electrophoresis and randomly amplified polymorphic DNA PCR.

Molecular strain typing by pulsed-field gel electrophoresis and by randomly amplified polymorphic DNA analysis was used to investigate a cluster of four Nocardia asteroides isolates associated with the BACTEC 460 TB system. An instrument motor drive misalignment resulted in inadequate needle sterilization and cross-contamination of BACTEC vials. This pseudo-outbreak illustrates the importance of proper BACTEC 460 needle sterilization and maintenance and confirms the usefulness of molecular typing methods for epidemiologic investigations.

Ribotyping: a tool for taxonomy and identification of the Nocardia asteroides complex species.

Ribotyping has been evaluated as a taxonomic tool for studying bacteria belonging to the Nocardia asteroides complex. The probe used was obtained by PCR from DNA extracted from the type strain Nocardia asteroides ATCC 19247, a sequence that codes partly for 16S rRNA. Interpretation of hybridization after EcoRI restriction of total DNA of 21 strains of the N. asteroides complex allowed for the identification of only four different ribotypes: two related to N. asteroides sensu stricto, one related to N. farcinica and one related to N. nova. These results confirm the classification established by Tsukamura in 1982 (M. Tsukamura, Microbiol. Immunol. 26:1101-1119, 1982) as well as the heterogeneity of N. asteroides sensu stricto species. Ribotyping may also provide a major identification technique for the species belonging to the N. asteroides complex.

DNA amplification and restriction endonuclease analysis for differentiation of 12 species and taxa of Nocardia, including recognition of four new taxa within the Nocardia asteroides complex.

Nineteen reference and 156 clinical strains of the genus Nocardia belonging to 12 taxonomic groups were studied for restriction fragment length polymorphism (RFLP) by using an amplified 439-bp segment of the 65-kDa heat shock protein gene. Of 30 restriction endonucleases, digestion with MspI and then digestion with BsaHI produced RFLP band patterns which separated all 12 groups except N. asteroides type IV from 6 of 12 N. transvalensis isolates and N. carnea from the N. asteroides type VI isolates. Commonly encountered species such as N. nova, N. farcinica, N. brasiliensis sensu stricto, and N. otitidiscaviarum were easily separated. Each taxon resulted in a single RFLP band pattern that included > or = 96% of all biochemically grouped isolates for 9 of 12 taxa with MspI and for 8 of 12 taxa with BsaHI. With the use of both patterns, only 6 of 175 (3.4%) isolates failed to fit the biochemically defined group patterns. These studies provide the first evidence for the separate identities of four antibiogram-defined (but currently unnamed) groups within the N. asteroides complex (types I, II, IV, and VI) and the presence of two subgroups within N. transvalensis. They also provide genotypic evidence for the separate identities of N. nova and N. farcinica. The lack of BstEII recognition sites in amplicons obtained from nocardiae provides a simple and rapid method for the differentiation of nocardiae from mycobacteria. DNA amplification with RFLP analysis is the first rapid method that distinguishes all clinically significant taxa and recognized species within the genus Nocardia.

Isolation, sequencing and expression of the superoxide dismutase-encoding gene (sod) of Nocardia asteroides strain GUH-2.

Nocardia asteroides (Na) superoxide dismutase (SOD) has been implicated as a virulence factor that allows the organism to survive intracellular killing by phagocytic cells. A full-length Na sod gene from a pathogenic strain of Na (strain GUH-2) was cloned from a recombinant phage library using the Mycobacterium tuberculosis (Mt) sod gene (Mt sod) as a probe. The promoter region and structural gene (624 bp) of Na sod was sequenced and nucleotide sequence comparisons reveal 77% homology with Mt sod. The Na sod gene also shares considerable sequence homology with sod of other mycobacterial species. In addition, conserved amino acid (aa) sequences important for metal binding indicate that Mn2+ is the preferred metal ion ligand for Na SOD. An Na sod expression plasmid, pYEX1, under transcriptional control of the Mt hsp70 promoter (pY6013), produced a 25-kDa protein product which showed SOD activity when stained in a native polyacrylamide gel and reacted with rabbit polyclonal antibody specific for Na SOD by Western blot. pYEX1, via transformation, was able to complement an Escherichia coli double sodAB mutant deficient in SOD production in the presence of paraquat (methyl viologen) which stimulates the production of superoxide radicals.

IS204: an insertion sequence from Nocardia asteroides (mexicana) YP21.

An insertion sequence was found in Nocardia asteroides YP21. The element, designated IS204, is 1452 bp long and has 19/23 bp imperfect inverted repeats at its ends. The sequences of IS204 terminal inverted repeats have high homology with those of IS1096 from Mycobacterium smegmatis. An 8-bp duplication of target sequence was found at the insertion site. Sequence analysis revealed that IS204 contains an open reading frame of 1134 bp, which encodes a putative transposase similar to those found in IS1096 and in Tn4652 from Pseudomonas sp. EST1001. At least nine copies of IS204 are present in the genome of N asteroides YP21. The plasmid pCY 104::IS204 could be inserted with another copy of IS204 at a different site. The possible mechanisms are discussed.

Site-specific growth of Nocardia asteroides in the murine brain.

The growth of Nocardia asteroides GUH-2 and two mutants (NG-49 and I-38-syn) in regions of the brains of BALB/c mice was determined by microdissection and viable counting. GUH-2 grew throughout the murine brain but at different growth rates that depended on the specific location. The rate of increase in total CFU per brain during GUH-2 infection was unaffected by the inoculum size; however, in five of eight brain regions, an alteration in the inoculum size resulted in altered nocardial growth rates. Mutant NG-49 showed a significantly slower rate of increase in total CFU per brain than did the parental strain, GUH-2, and significantly decreased growth rates in seven brain regions. Mutant I-38-syn showed a rate of increase in total CFU per brain similar to that of the parental strain; however, this mutant grew significantly faster in the cerebellum and pons-medulla. Growth appeared to be a necessary precursor to the cellular damage that resulted in the variety of neurological disorders observed in mice infected with N. asteroides GUH-2, because mutant NG-49 exhibited a decreased ability to grow in specific regions of the brain and did not induce signs of neurological damage. In contrast, mutant I-38-syn induced neurological signs in a larger percentage of the infected animals than did parental strain GUH-2 and grew better in certain regions of the brain than did the parental strain. Furthermore, there appeared to be a relationship between the growth of N. asteroides in the substantia nigra and the induction of an L-dopa-responsive head shake that was observed in some of the mice following a sublethal intravenous injection of N. asteroides GUH-2.