Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica.

We identified the biosynthetic gene clusters of the siderophore nocobactin NA. The nbt clusters, which were discovered as genes highly homologous to the mycobactin biosynthesis genes by the genomic sequencing of Nocardia farcinica IFM 10152, consist of 10 genes separately located at two genomic regions. The gene organization of the nbt clusters and the predicted functions of the nbt genes, particularly the cyclization and epimerization domains, were in good agreement with the chemical structure of nocobactin NA. Disruptions of the nbtA and nbtE genes, respectively, reduced and abolished the productivity of nocobactin NA. The heterologous expression of the nbtS gene revealed that this gene encoded a salicylate synthase. These results indicate that the nbt clusters are responsible for the biosynthesis of nocobactin NA. We also found putative IdeR-binding sequences upstream of the nbtA, -G, -H, -S, and -T genes, whose expression was more than 10-fold higher in the low-iron condition than in the high-iron condition. These results suggest that nbt genes are regulated coordinately by IdeR protein in an iron-dependent manner. The ΔnbtE mutant was found to be impaired in cytotoxicity against J774A.1 cells, suggesting that nocobactin NA production is required for virulence of N. farcinica.

Functional analysis of a small cryptic plasmid pYS1 from Nocardia.

Bacteria of the genus Nocardia cause opportunistic infections of lung, brain and central nervous system, and cutaneous tissue. They are also producers of antibiotics and industrially important enzymes. As studies describing plasmids in this genus are limited, we have characterized a 4326bp cryptic plasmid pYS1 from Nocardia aobensis IFM 10795. Three open reading frames (ORFs) were predicted. Both sequence analyses and detection of single-stranded intermediates suggested a rolling-circle mechanism as the mode of replication of pYS1. Mutageneses and deletion analyses revealed both the predicted double- and single-stranded origins to be indispensable in replication, suggesting a lack of secondary signals for leading and lagging strand synthesis. The replicon of pYS1 is broad-host-range and compatible to that of pAL5000 of mycobacteria, making it potentially useful in genetic manipulation of various actinomycetes. Insertion analyses showed orf1, despite its sequence similarity to plasmid transfer genes, is involved in plasmid stability rather than conjugation and is lethal in the absence of a functional orf3. This situation is somewhat analogous to the kil/kor system of pIJ101 of Streptomyces, except that orf3 was unrelated to korA and was shown by promoter-probe assays to encode a novel transcriptional repressor negatively regulating orf1 expression.

Systemic nocardiosis caused by Nocardia concava in China.

A 42-year-old man with polychondritis and a 2-year history of using low-dose prednisone and other immunosuppressive drugs was admitted to our hospital due to persistent high fever of 10 days duration. A strain of Nocardia was twice isolated from his blood and subsequently identified to be N. concava. The patient was initially treated with sulphadiazine sodium, vancomycin and imipenema for 7 days but the symptoms persisted. Consequently, the regimen was changed to sulphadiazine sodium, ciprofloxacin and amikacin sulfate based on the antibiotic susceptibility tests of the Nocardia isolate. The fever disappeared and the patient's condition improved after 10 days of this treatment to the extent that he was discharged. However, 7 days later, the patient's condition deteriorated and he died due to multiple organ failure. This is the first report of N. concava causing systemic nocardiosis in China.

Pulmonary nocardiosis caused by Nocardia exalbida complicating Pneumocystis pneumonia in an HIV-infected patient.

A 47-year-old man with optimally controlled type-2 diabetes mellitus and chronic hepatitis B was admitted to a local hospital because of a 1-week history of cough and high-grade fever. He was diagnosed with Pneumocystis pneumonia (PCP) and Klebsiella pneumonia from a chest radiograph and sputum. Simultaneously, he was found to have HIV infection with a CD4 count of 76/µl. Despite alteration of treatment secondary to the development of allergic reaction to trimethoprim-sulfamethoxazole (TMP-SMX), the patient was able to complete a 3-week therapy for PCP after being switched to pentamidine isetionate. After the treatment of PCP, he was referred to our hospital for the initiation of anti-HIV therapy. He presented with recurrent high-grade fever of a few days' duration prior to his initial visit, which subsequently led to his admission. Chest computed tomography (CT) showed the enlargement of a previously identified infiltrate in the left upper lung field, and the sputum culture upon admission was positive for Gram-positive branching rods; the organism was later identified as Nocardia exalbida. Due to his allergy to sulfonamide, the patient was treated with imipenem (IMP) and amikacin (AMK) given intravenously for 17 days, followed by garenoxacin (GRNX) taken orally for 6 months, without any adverse effects. The chest infiltrate resolved completely, and he remains stable without relapse 8 months after the completion of the therapy. Pulmonary nocardiosis should be considered as a differential diagnosis of recurring pneumonia in immunocompromised patients, especially in HIV-infected individuals. Oral administration of GRNX following IMP and AMK can be used as an alternative to TMP-SMX therapy in cases of pulmonary nocardiosis caused by N. exalbida.

Lymphocutaneous type of nocardiosis caused by Nocardia vinacea in a patient with polymyositis.

We report a lymphocutaneous type of nocardiosis caused by Nocardia vinacea. A 62-year-old woman with polymyositis presented with some erythematous swellings and subcutaneous abscesses on her right middle finger and the dorsum of her hand, which had persisted for 2 weeks. Culturing of the excised nodule and pus revealed orange to orange-tan colonies with scanty whitish aerial mycelia. The isolate was identified as N. vinacea on the basis of its biochemical and chemotaxonomic characteristics and the results of molecular biological analysis. In our case, oral minocycline (MINO) and trimethoprim-sulfamethoxazole (TMP-SMX) for 7 weeks did not improve the clinical manifestation, even though in vitro susceptibility testing of the isolate predicted its susceptibility to MINO and TMP-SMX. Treatment with partial surgical excision followed by TMP-SMX and meropenem administration was effective. This is the first reported case of a lymphocutaneous type of nocardiosis caused by N. vinacea.

Homozygous triplicate mutations in three 16S rRNA genes responsible for high-level aminoglycoside resistance in Nocardia farcinica clinical isolates from a Canada-wide bovine mastitis epizootic.

Nocardia farcinica strains showing high-level resistance to amikacin were isolated from clinical cases in a Canada-wide bovine mastitis epizootic. Shotgun cloning of the resistance genes in the amikacin-resistant mastitis isolate N. farcinica IFM 10580 (W6220 [Centers for Disease Control and Prevention]) using a multicopy vector system revealed that the 16S rRNA gene with an A-to-G single-point mutation at position 1408 (in Escherichia coli numbering) conferred "moderate" cross-resistance to amikacin and other aminoglycosides to an originally susceptible N. farcinica strain IFM 10152. Subsequent DNA sequence analyses revealed that, in contrast to the susceptible strain, all three chromosomal 16S rRNA genes of IFM 10580, the epizootic clinical strain, contained the same A1408G point mutations. Mutant colonies showing high-level aminoglycoside resistance were obtained when the susceptible strain N. farcinica IFM 10152 was transformed with a multicopy plasmid carrying the A1408G mutant 16S rRNA gene and was cultured in the presence of aminoglycosides for 3 to 5 days. Of these transformants, at least two of the three chromosomal 16S rRNA genes contained A1408G mutations. A triple mutant was easily obtained from a strain carrying the two chromosomal A1408G mutant genes and one wild-type gene, even in the absence of the plasmid. The triple mutant showed the highest level of resistance to aminoglycosides, even in the absence of the plasmid carrying the mutant 16S rRNA gene. These results suggest that the homozygous mutations in the three 16S rRNA genes are responsible for the high-level aminoglycoside resistance found in N. farcinica isolates of the bovine mastitis epizootic.

Characterization of clinical isolates of Gordonia species in Japanese clinical samples during 1998-2008.

During 1998-2008, there were 31 strains of Gordonia species isolated from clinical specimens in our laboratory. Our identification of the 31 strains of Gordonia species showed that major pathogenic Gordonia species in Japan were classifiable, respectively into 14 and 13 strains of Gordonia sputi and Gordonia bronchialis. The four remaining strains were identified as three Gordonia species: G. aichiensis (2 strains), and G. terrae (1 strain), and G. otitidis (1 strain). Results of drug susceptibility tests for these 31 strains of Gordonia isolates are reported herein.

Identification of Nocardia farcinica by a PCR primer amplifying a specific DNA band for the bacterium.

A PCR primer specific to Nocardia farcinica was prepared based on sequence information of random amplified polymorphic DNA (RAPD) analysis. The PCR primer amplifies N. farcinica species only; no amplification was observed in 25 other Nocardia strains that we tested. Specificity of the primer for N. farcinica was also confirmed using other fungal and bacterial strains that are frequently isolated from clinical samples such as sputa and broncho alveolar lavage (VAL).

Transvalencin Z, a new antimicrobial compound with salicylic acid residue from Nocardia transvalensis IFM 10065.

Transvalencin Z was isolated from a culture broth of Nocardia transvalensis IFM 10065, a clinical isolate from a Japanese patient with actinomycotic mycetoma. The transvalencin Z structure was determined using NMR and mass spectrometric analyses. The structure is similar to a partial structure of siderophores such as mycobactins and nocobactins, but the compound has no cytotoxic activity. Transvalencin Z shows a strong antimicrobial activity against Gram-positive bacteria, but shows no activity against Gram-negative bacteria, fungi and tumor cells.

First clinical isolates of Nocardia carnea, Nocardia elegans, Nocardia paucivorans, Nocardia puris and Nocardia takedensis in Japan.

Five aerobic actinomycete strains isolated from patients in Japan were assigned provisionally to the genus Nocardia based on morphological and physiological characteristics. The five strains, IFM 10481, IFM 0668, IFM 0901, IFM 0583 and IFM 0342, were not classified into any Nocardia species reported as infectious agents in Japan. Therefore, they were studied further to determine their specific taxonomic positions. Detailed chemotaxonomic and physiologic characterization and 16S rDNA sequence data of the five strains showed that they belonged to respective species of Nocardia carnea, N. elegans, N. paucivorans, N. puris and N. takedensis. This is the first isolation report of these five Nocardia species from patients in Japan.

Biotransformation of bile acids by pathogenic actinomycetes Nocardia otitidiscaviarum and Amycolatopsis sp. strains.

Three sterol-type compounds (compounds 4, 5 and 6) were isolated from culture broth of pathogenic Nocardia otitidiscaviarum IFM 0988 and Amycolatopsis sp. IFM 0703 strains which were isolated from Japanese patients. The structures of the compounds were determined by NMR and mass spectrometric analyses. The structural studies indicated that compound 4 is a biotransformation product from cholic acid derivative in a nutrient culture medium constituent by a reductase-type enzyme, and the remaining two compounds 5 and 6 are also biotransformation ones by oxidase-type enzymes.

Nocardia anaemiae sp. nov. isolated from an immunocompromised patient and the first isolation report of Nocardia vinacea from humans.

Two actinomycete strains that were isolated from patients in Japan were assigned provisionally to the genus Nocardia based on their morphological characteristics. The two isolates were further studied to determine their specific taxonomic status. Detailed chemotaxonomic characterization and 16S rDNA sequence data for the strains showed that they are most similar to Nocardia vinacea. DNA-DNA hybridization experiments indicated that strain IFM 0344 should be identified as N. vinacea, and that strain IFM 0323T is classifiable as a new species. This report describes the first isolation of N. vinacea from clinical samples. A new species of the genus Nocardia is proposed based on their phenotypic and phylogenetic characteristics: Nocardia anaemiae for IFM 0323T (=NBRC 100462T=JCM 12396T=DSM 44821T).

MOLECULAR IDENTIFICATION AND ANTIMICROBIAL RESISTANCE PATTERN OF SEVEN CLINICAL ISOLATES OF Nocardia spp. IN BRAZIL.

Nocardia is a ubiquitous microorganism related to pyogranulomatous infection, which is difficult to treat in humans and animals. The occurrence of the disease is on the rise in many countries due to an increase in immunosuppressive diseases and treatments. This report of cases from Brazil presents the genotypic characterization and the antimicrobial susceptibility pattern using the disk-diffusion method and inhibitory minimal concentration with E-test® strips. In summary, this report focuses on infections in young adult men, of which three cases were cutaneous, two pulmonary, one neurological and one systemic. The pulmonary, neurological and systemic cases were attributed to immunosuppressive diseases or treatments. Sequencing analysis of the 16S rRNA segments (1491 bp) identified four isolates of Nocardia farcinica, two isolates of Nocardia nova and one isolate of Nocardia asiatica. N. farcinica was involved in two cutaneous, one systemic and other pulmonary cases; N. nova was involved in one neurological and one pulmonary case; and Nocardia asiatica in one cutaneous case. The disk-diffusion antimicrobial susceptibility test showed that the most effective antimicrobials were amikacin (100%), amoxicillin/clavulanate (100%), cephalexin (100%) and ceftiofur (100%), while isolates had presented most resistance to gentamicin (43%), sulfamethoxazole/trimethoprim (43%) and ampicillin (29%). However, on the inhibitory minimal concentration test (MIC test), only one of the four isolates of Nocardia farcinica was resistant to sulfamethoxazole/trimethoprim.

Brasilicardin A. A Novel Tricyclic Metabolite with Potent Immunosuppressive Activity from Actinomycete Nocardiabrasiliensis.

A novel tricyclic metabolite, brasilicardin A (1), with potent immunosuppressive activity has been isolated from the cultured broth of the actinomycete Nocardia brasiliensis IFM 0406, and the structure including absolute stereochemistry was established on the basis of spectroscopic data, chemical means, and X-ray analysis. Brasilicardin A (1) is the first tricyclic compound consisting of an anti/syn/anti-perhydrophenanthrene skeleton with a rhamnose, an N-acetylglucosamine, and an amino acid moiety.

Isolation and structural characterization of siderophores, madurastatins, produced by a pathogenic Actinomadura madurae.

Madurastatins Al (1), A2 (2) and A3 (3), novel pentapeptides that were acylated with salicylic acid at the N-terminus, were isolated from the culture broth of a pathogenic Actinomadura madurae IFM 0745 strain. These structures were mainly determined by 2D NMR and MS/MS spectral techniques. The strain produced simultaneously madurastatins B1 (4) and B2 (5) consisting of Ser and salicylic acid moieties. Compounds 1 and 4 had an antibacterial activity against Micrococcus luteus, indicating that the presence of the aziridine ring is essential for such activity. Because 1 has a strong affinity with ferric ion due to the presence of two hydroxamic acids and a salicylic acid, it is considered to be a siderophore that is a low molecular weight iron chelater. The production of siderophores may be one of the characteristics of pathogenic microorganisms.

Transvalencin A, a thiazolidine zinc complex antibiotic produced by a clinical isolate of Nocardia transvalensis. I. Taxonomy, fermentation, isolation and biological activities.

A new thiazolidine-type antibiotic with zinc in its structure, designated transvalencin A, was isolated from Nocardia sp. IFM 10065, a clinical isolate from a patient with actinomycotic mycetoma. The strain was identified as Nocardia transvalensis based on its morphological, phenotypic and phylogenetic characteristics. Transvalencin A showed antimicrobial activity against fungi such as Trichophyton mentagrophytes and Cryptococcus neoformans. The antibiotic is also active against Gram-positive bacteria such as Micrococcus luteus. We observed higher activity for fungi in an acidic medium than in a neutral medium.

Transvalencin A, a thiazolidine zinc complex antibiotic produced by a clinical isolate of Nocardia transvalensis. II. Structure elucidation.

A novel antifungal antibiotic, transvalencin A, is produced by Nocardia transvalensis IFM 10065 isolated from a patient with actinomycotic mycetoma in Japan. The antibiotic structure was elucidated using NMR, mass spectrometric investigations, and X-ray crystallographic analysis. Transvalencin A is a 1:1 complex of a zinc and an organic acid with a phenolic substituent. Transvalencin A is comprised of o-substituted p-chlorophenol, tetrasubstituted oxazoline, disubstituted thiazolyl-N-methylthiazolidine and monosubstituted N-methylthiazolidine.

First isolates of Nocardia abscessus from humans and soil in Japan.

Nocardia abscessus, a recently established species, was isolated from patients during 2000. In the course of our taxonomic studies on 121 clinical Nocardia isolates in Japan 5 strains isolated from patients plus one strain isolated from soil in Japan, were found to have similar physiological characteristics to those of N. abscessus. Phylogenetic studies using 16S rRNA gene sequence analysis confirmed that these strains belong to N. abscessus. This is the first isolation report of N. abscessus from soil as well as from clinical samples in Japan.

Molecular identification and antimicrobial susceptibility of Nocardia spp. isolated from bovine mastitis in Brazil.

Nocardia spp. infections can cause severe damage to the mammary gland due to suppurative pyogranulomatous lesions and lack of clinical cure in response to conventional antimicrobial therapy. Although Nocardia infections are considered relatively uncommon in cows, there has been an apparent worldwide increase in the incidence of bovine mastitis caused by Nocardia spp, perhaps due to environmental transmission of this ubiquitous pathogen. The objectives of present study were to determine: (i) species distribution of 80 Nocardia isolates involved in bovine mastitis (based on molecular methods); and (ii) antimicrobial susceptibility pattern of all isolates from three geographical areas in Brazil. In this study, Nocardia nova (80%) was the most frequently isolated species, followed by Nocardia farcinica (9%). Additionally, Nocardia puris, Nocardia cyriacigeorgica, Nocardia veterana, Nocardia africana, and Nocardia arthritidis were detected using 16S rRNA sequencing. This is apparently the first report of N. puris, N. veterana, N. cyriacigeorgica, N. arthritidis and N. africana in association with bovine mastitis. Based on the disk diffusion test, isolates were most frequently resistant to cloxacillin (75%), ampicillin (55%) and cefoperazone (47%), whereas few Nocardia spp. were resistant to amikacin, cefuroxime or gentamicin.

Disseminated Nocardiosis caused by Nocardia concava with acute respiratory failure and central nervous system involvement treated with linezolid.

Nocardia concava was identified as a new species in 2005; however, the clinical manifestations of Nocardia concava infection have yet to be clarified. We herein present the case of an immunosuppressed patient who developed disseminated nocardiosis caused by N. concava with multiple abscesses in the lungs, cutis, subcutaneous tissue, skeletal muscles and kidneys accompanied by central nervous system involvement, including meningitis and ventriculitis. The patient was cured with appropriate treatment including linezolid after testing for susceptibility. Linezolid should be considered as an alternative agent for treating disseminated nocardiosis because of its effective distribution to multiple sites.