Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens

Intra-abdominal nocardiosis and scedosporiosis in a dog: case report and literature review

A 2-y-old, intact female, mixed-breed dog was presented to the veterinary hospital with abdominal distension, anemia, and lethargy following a chronic history of nonspecific gastrointestinal signs. CBC and serum biochemistry revealed moderate nonregenerative anemia with neutrophilia, hypoalbuminemia, hyperglobulinemia, hypoglycemia, decreased urea and creatinine, and hypercholesterolemia. Abdominal radiographs and ultrasound revealed a large heterogeneous mesenteric mass and ascites. Abdominocentesis confirmed septic peritonitis with filamentous bacteria. Fine-needle aspiration of the mass yielded pyogranulomatous inflammation and hyphae. An exploratory laparotomy revealed a large cranial abdominal mass with granulomas present throughout the abdominal cavity. Due to the poor prognosis and disseminated disease, the owner elected euthanasia. Postmortem and histologic examinations detected intralesional mycetomas and bacterial colonies within the mesenteric masses. 16S ribosomal RNA gene PCR and sequencing using formalin-fixed, paraffin-embedded sections identified Nocardia yamanashiensis, Nocardioides cavernae, and Nocardioides zeicaulis. Fungal culture, PCR, and sequencing confirmed Scedosporium apiospermum. Our report highlights the importance of molecular methods in conjunction with culture and histologic findings for diagnosing coinfections caused by infrequent etiologic agents. Additionally, we provide a comprehensive literature review of Scedosporium apiospermum infections in dogs.

Nocardia acididurans sp. nov., an acid-tolerant actinobacterium isolated from bio-fertilizer of Musa species

A novel acid-tolerant actinobacterium (strain LPG 2^T), which formed fragmented substrate mycelia, was isolated from bio-fertiliser of Musa spp. collected from Lampang Province, Thailand. Its morphological and chemotaxonomic properties, e.g., the presence of mycolic acid and MK-8 (H_4ω-cycl) in the cells, showed that strain LPG 2^T was a member of the genus Nocardia. 16S rRNA gene sequence analysis revealed that this strain was closely related to Nocardia otitidiscaviarum NBRC 14405^T (98.7 %). The low average nucleotide identity-blast and digital DNA-DNA hybridization values (<78.6 and <24.0 %, respectively), and several phenotypic differences between strain LPG 2^T and its related Nocardia type strains, indicated that the strain merits classification as representing a novel species of the genus Nocardia, for which we propose the name Nocardia acididurans sp. nov. The type strain is LPG 2^T (=TBRC 11242^T=NBRC 114293^T).

Nocardia huaxiensis sp. nov., an actinomycete isolated from human skin

A novel actinomycete, designated as strain WCH-YHL-001^T, was isolated from skin biopsy specimens of a patient at West China Hospital, Chengdu, Sichuan Province, PR China. The cells were Gram-positive, aerobic, heterotrophic and non-motile. They formed an extensive substrate with short aerial mycelia, whose branches fragmented into rod-shaped elements. Growth occurred at 10-40 °C, pH 5.0-12.0 and with NaCl concentrations of 0-4.0 % (w/v). The major cellular fatty acids of strain WCH-YHL-001^T were C_16 : 0, C_18 : 1  ω9c, C_18 : 0 10-methyl and summed feature 3. The predominant respiratory quinone was MK-8 (H4ω-cycl). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol mannoside, unknown phospholipids and unidentified glycolipids. The diagnostic diamino acid of peptidoglycan was meso-diaminopimelic acid. The whole-cell sugar pattern consisted of arabinose and glucose. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain WCH-YHL-001^T belonged to the genus Nocardia. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strain WCH-YHL-001^T and type strains of Nocardia species were lower than the cut-offs (≥95-96 % for ANI and ≥70 % for isDDH) required to define a bacterial species. The genomic DNA G+C content was 67.8 mol%. Phylogenetic, physiological and chemotaxonomic data suggested that strain WCH-YHL-001^T represented a novel species of the genus Nocardia, for which the name Nocardia huaxiensis sp. nov. is proposed, with the type strain WCH-YHL-001^T (=GDMCC 4.181^T=JCM 34475 ^T=NBRC 114973^T).

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Genomic characterization of Nocardia seriolae strains isolated from diseased fish

Members of the genus Nocardia are widespread in diverse environments; a wide range of Nocardia species are known to cause nocardiosis in several animals, including cat, dog, fish, and humans. Of the pathogenic Nocardia species, N. seriolae is known to cause disease in cultured fish, resulting in major economic loss. We isolated two N. seriolae strains, CK‐14008 and EM15050, from diseased fish and sequenced their genomes using the PacBio sequencing platform. To identify their genomic features, we compared their genomes with those of other Nocardia species. Phylogenetic analysis showed that N. seriolae shares a common ancestor with a putative human pathogenic Nocardia species. Moreover, N. seriolae strains were phylogenetically divided into four clusters according to host fish families. Through genome comparison, we observed that the putative pathogenic Nocardia strains had additional genes for iron acquisition. Dozens of antibiotic resistance genes were detected in the genomes of N. seriolae strains; most of the antibiotics were involved in the inhibition of the biosynthesis of proteins or cell walls. Our results demonstrated the virulence features and antibiotic resistance of fish pathogenic N. seriolae strains at the genomic level. These results may be useful to develop strategies for the prevention of fish nocardiosis.

Nocardia yamanashiensis in an immunocompromised patient presenting as an indurated nodule on the dorsal hand

Background

Nocardia are ubiquitous, aerobic, gram-positive actinomycetes. Nocardiosis typically occurs in immunocompromised patients, although immunocompetent individuals can also be affected.

Purpose

The purpose of this case study is to review the clinical characteristics and treatments of a unique form of cutaneous nocardiosis.

Materials and Methods

We retrospectively reviewed the medical literature using PubMed, searching the terms cutaneous, host, immunocompromised, Nocardia, primary, yamanashiensis. Patient reports and previous reviews of the subject were critically assessed and the salient features are presented.

Results

Cutaneous nocardiosis typically presents as pustular nodules and the lesions may progress to become abscesses, cellulitis, granulomas or keloid-like tumors. N. brasiliensis is the predominant species involved in primary cutaneous nocardiosis; other common Nocardia species involved in human disease are N. farcinica, N. abscessus, N. cyriacigeorgica, and N. nova. Only two individuals (including the patient presented here) with primary cutaneous infection by N. yamanashiensis have been described in the literature; a third clinical isolate was recovered from a lung biopsy.

Conclusion

Nocardia yamanashiensis is a rare clinical form of primary cutaneous nocardiosis. 16S ribosomal gene sequencing, as well as Gram stain and modified Fite acid-fast stain, play a vital role in identifying this clinical variant.

Nocardiosis from 1888 to 2017

The genus Nocardia is an aerobic bacterium, Gram-positive and catalase positive that is in Nocardiaceae family. This bacterium first described by Edmond Nocard in 1888 and is not in human commensal bacteria. To date, nocardiosis incidence is increasing due to increase population growth rate, increase in patients with immune disorder diseases and immunocompromised patients. We surveyed taxonomic position, isolation methods, phenotypic and molecular identification at the genus and species levels, antibiogram, treatment and epidemiology in the world from 1888 to 2017.

Broad Spectrum Antimicrobial Activity of Forest-Derived Soil Actinomycete, Nocardia sp. PB-52

A mesophilic actinomycete strain designated as PB-52 was isolated from soil samples of Pobitora Wildlife Sanctuary of Assam, India. Based on phenotypic and molecular characteristics, the strain was identified as Nocardia sp. which shares 99.7% sequence similarity with Nocardia niigatensis IFM 0330 (NR_112195). The strain is a Gram-positive filamentous bacterium with rugose spore surface which exhibited a wide range of antimicrobial activity against Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA), Gram-negative bacteria, and yeasts. Optimization for the growth and antimicrobial activity of the strain PB-52 was carried out in batch culture under shaking condition. The optimum growth and antimicrobial potential of the strain were recorded in GLM medium at 28°C, initial pH 7.4 of the medium and incubation period of 8 days. Based on polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) gene-targeted PCR amplification, the occurrence of both of these biosynthetic pathways was detected which might be involved in the production of antimicrobial compounds in PB-52. Extract of the fermented broth culture of PB-52 was prepared with organic solvent extraction method using ethyl acetate. The ethyl acetate extract of PB-52 (EA-PB-52) showed lowest minimum inhibitory concentration (MIC) against S. aureus MTCC 96 (0.975 μg/mL) whereas highest was recorded against Klebsiella pneumoniae ATCC 13883 (62.5 μg/mL). Scanning electron microscopy (SEM) revealed that treatment of the test microorganisms with EA-PB-52 destroyed the targeted cells with prominent loss of cell shape and integrity. In order to determine the constituents responsible for its antimicrobial activity, EA-PB-52 was subjected to chemical analysis using gas chromatography-mass spectrometry (GC-MS). GC-MS analysis showed the presence of twelve different chemical constituents in the extract, some of which are reported to possess diverse biological activity. These results confirmed that the presence of bioactive constituents in EA-PB-52 could be a promising source for the development of potent antimicrobial agents effective against wide range of microbial pathogens including MRSA.

Identification of Nocardia species using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry

BACKGROUND

The MALDI (matrix-assisted laser desorption/ionization) Biotyper system for bacterial identification has already been utilized in clinical microbiology laboratories as a successful clinical application of protoemics. However, in cases of Nocardia, mass spectra suitable for MALDI Biotyper identification are often not obtained if such specimens are processed like general bacteria. This problem is related to the insufficiencies in bacterial spectrum databases that preclude accurate specimen identification. Here, we developed a bacterial processing method to improve mass spectra from specimens of the genus Nocardia. In addition, with the new processing method, we constructed a novel in-house bacterial database that combines a commercial database and mass spectra of Nocardia strains from the Department of Clinical Laboratory at Chiba University Hospital (DCLC) and the Medical Mycology Research Center at Chiba University (MMRC).

RESULTS

The newly developed method (Nocardia Extraction Method at DCLC [NECLC]) based on ethanol-formic acid extraction (EFAE) improved mass spectra obtained from Nocardia specimens. The Nocardia in-house database at Chiba University Hospital (NDCUH) was then successfully validated. In brief, prior to introduction of the NECLC and NDCUH, 10 of 64 (15.6%) clinical isolates were identified at the species level and 16 isolates (25.0%) could only be identified at the genus level. In contrast, after the introduction, 58 isolates (90.6%) were identified at the species level and 6 isolates (9.4%) were identified at the genus level.

CONCLUSIONS

The results of this study suggest that MALDI-TOF (time-of-flight) Biotyper system can identify Nocardia accurately in a short time in combination with a simple processing method and an in-house database.

Nocardiosis in 132 patients with cancer: microbiological and clinical analyses

OBJECTIVES

To correlate the microbiological and clinical features of infections caused by Nocardia species.

METHODS

We determined the species and drug susceptibility of 138 Nocardia strains isolated from 132 patients at the University of Texas M. D. Anderson Cancer Center (Houston, TX) from 2002 through 2012 and analyzed the clinical features.

RESULTS

The 132 patients included 82 men and 50 women with a mean age of 59.1 years. All except two had underlying cancer, and 47 (35.6%) also received a stem cell transplant. These patients experienced 136 episodes of Nocardia infection, including pulmonary infection, abscess of deep skin and soft tissue, bacteremia and dissemination, and brain abscess. The 138 Nocardia strains involved 27 species, of which 20 species have been described since 2000. Common species included Nocardia nova, Nocardia cyriacigeorgica, Nocardia farcinica, and Nocardia abscessus, together accounting for 59.4%. N nova caused most bacteremia cases, whereas N farcinica caused most of the skin and brain infections. Infections with a few recent species likely represented first confirmation or report of human infections. Antimicrobial susceptibility tests of 117 strains showed that they were all susceptible to trimethoprim-sulfamethoxazole and linezolid but variably susceptible to other drugs depending on species. Most patients who were treated for the infection showed improvement or resolution.

CONCLUSIONS

Diverse Nocardia species can cause secondary infections in patients with cancer. Timely species identification and antimicrobial susceptibility tests may guide treatment.

Primary brain abscess caused by Nocardia otitidiscaviarum

Diagnosing primary cerebral nocardiosis is difficult. This case report describes a 79-year-old immunocompetent Japanese woman with a primary brain abscess caused by Nocardia otitidiscaviarum (IFM 11321) and reviews the findings of 11 previous patients with N. otitidiscaviarum-induced brain abscesses. Four patients survived, including ours. Beta-lactams were not effective in our patient, and the diagnosis required a pathologic analysis of the surgical specimen. Sulfamethoxazole/trimethoprim (ST) was administered to the patient. On antibiotic susceptibility testing, N. otitidiscaviarum (IFM11321) was found to be resistant to amoxicillin-clavulanic acid, ceftriaxone, cefotaxime, cefepime, imipenem and clarithromycin, but sensitive to amikacin, gentamicin, ST and linezolid. Antimicrobial susceptibility patterns differ among Nocardia species, making species identification important for treatment. Patients with suspected Nocardia infection should therefore be treated empirically with ST and/or amikacin and considered for surgical management.

Mycetoma caused by Nocardia yamanashiensis, Papua New Guinea

We report the first documented case of a mycetoma caused by Nocardia yamanashiensis after the initial description of this species. The 16S-rRNA gene sequence analysis was used to identify the novel species, which showed a similarity of 99.9% to the gene sequence of the type strain. The case showed both clinical non-response and reduced susceptibility in vitro to amoxicillin plus clavulanate, and it was treated successfully with trimethoprim-sulfamethoxazole and doxycycline. Given antibiotic resistance concerns, we suggest that antimicrobial susceptibility testing should be done for the majority of Nocardia species without well-established resistance patterns.

Antibiofilm activity of Streptomyces sp. BFI 230 and Kribbella sp. BFI 1562 against Pseudomonas aeruginosa

Members of the actinomycetes family are a rich source of bioactive compounds including diverse antibiotics. This study sought to identify novel and non-toxic biofilm inhibitors from the actinomycetes library for reducing the biofilm formation of Pseudomonas aeruginosa PAO1. After the screening of 4104 actinomycetes strains, we found that the culture spent medium (1 %, v/v) of Streptomyces sp. BFI 230 and Kribbella sp. BFI 1562 inhibited P. aeruginosa biofilm formation by 90 % without affecting the growth of planktonic P. aeruginosa cells, while the spent media enhanced the swarming motility of P. aeruginosa. Global transcriptome analyses revealed that the spent medium of Streptomyces sp. BFI 230 induced expression of phenazine, pyoverdine, pyochelin synthesis genes, and iron uptake genes in P. aeruginosa. The addition of exogenous iron restored the biofilm formation and swarming motility of P. aeruginosa in the presence of the spent medium of Streptomyces sp. BFI 230, which suggests that the Streptomyces sp. BFI 230 strain interfered iron acquisition in P. aeruginosa. Experiments on solvent extraction, heat treatment, and proteinase K treatment suggested that hydrophilic compound(s), possibly extracellular peptides or proteins from Streptomyces sp. BFI 230 cause the biofilm reduction of P. aeruginosa. Together, this study indicates that actinomycetes strains have an ability to control the biofilm of P. aeruginosa.

Nocardia endophytica sp. nov., an endophytic actinomycete isolated from the oil-seed plant Jatropha curcas L

A novel actinomycete, designated strain KLBMP 1256T, was isolated from a surface-sterilized stem of the oil-seed plant Jatropha curcas L. collected from Sichuan Province, south-west China, and was characterized to determine its taxonomic position. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate was closely related to members of the genus Nocardia in the family Nocardiaceae, being most closely related to Nocardia callitridis CAP 290T (98.4 % similarity) and Nocardia nova JCM 6044T (97.5 %). Levels of 16S rRNA gene sequence similarity between strain KLBMP 1256T and the type strains of other recognized species of the genus Nocardia were less than 97 %. Chemotaxonomic data supported the affiliation of the new isolate to the genus Nocardia. However, the novel strain could be distinguished from its closest phylogenetic neighbour, N. callitridis CAP 290T, by a range of phenotypic properties. The combination of low DNA–DNA relatedness values and phenotypic differences from N. callitridis CAP 290T indicated that strain KLBMP 1256T represents a novel species of the genus Nocardia, for which the name Nocardia endophytica sp. nov. is proposed. The type strain is KLBMP 1256T ( = KCTC 19777T  = CCTCC AA 2010004T).

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.

In vitro activity of multiple antibiotic combinations against Nocardia: relationship with a short-term treatment strategy in heart transplant recipients with pulmonary nocardiosis

BACKGROUND/OBJECTIVES

Pulmonary nocardiosis (PN) chiefly affects immunocompromised patients, particularly transplant recipients. Cotrimoxazole is still the mainstay of treatment, but it is associated with nephro- and myelo-toxicity, and can show unpredictable activity against Nocardia isolates.

METHODS

Over a 20-year period, Nocardia isolates were identified from 12 heart transplant (HTx) recipients with PN. The in vitro activity of various antibacterials, alone or in combination, was assessed using disk-diffusion, minimal inhibitory concentration (MIC), and time-kill methodology. The in vitro results were compared with the clinical outcome of the patients.

RESULTS

Seven different Nocardia strains were identified. Disk diffusion and MIC determinations showed that all isolates were susceptible to amikacin, netilmicin, and linezolid, and that moxifloxacin was the most active of the fluoroquinolones. All but 1 of the isolates were susceptible to imipenem. Time-kill studies showed that imipenem/amikacin and imipenem/moxifloxacin combinations were bactericidal for most isolates. Of 12 patients who received 3-4 weeks' intravenous (IV) treatment with amikacin or ciprofloxacin in combination with a beta-lactam, followed by 1-3 months' oral cotrimoxazole, moxifloxacin, or linezolid, 11 were cured; 1 patient died, but not related to Nocardia.

CONCLUSION

Initial PN treatment in HTx recipients can be successfully carried out with bactericidal combinations such as imipenem plus amikacin or moxifloxacin, administered IV for 3-4 weeks. Within 1 month, a significant clinical and radiological improvement may be observed. In our experience, a <3 month oral regimen with cotrimoxazole, moxifloxacin, or doxycycline may then be used. This may allow a reduction of side effects and treatment-related burden, without any recurrence.

Streptomyces coacervatus sp. nov., isolated from the intestinal tract of Armadillidium vulgare

A Gram-staining-positive bacterium, designated AS-0823(T), which formed spiral spore chains on the aerial mycelium, was isolated from the intestinal tract of Armadillidium vulgare, a small terrestrial crustacean commonly found on the ground around houses in Japan. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Streptomyces and was most closely related to Streptomyces longisporus ISP 5166(T) (98.6 % 16S rRNA gene sequence similarity), Streptomyces curacoi NBRC 12761(T) (98.4 %) and Streptomyces griseoruber NBRC 12873(T) (98.4 %). The affiliation of strain AS-0823(T) to the genus Streptomyces was supported by chemotaxonomic data: iso-C(16 : 0), anteiso-C(15 : 0), C(16 : 0), iso-C(15 : 0) and anteiso-C(17 : 0) as the major cellular fatty acids, ll-diaminopimelic acid as the characteristic diamino acid in the peptidoglycan and the absence of mycolic acids. DNA-DNA hybridization and physiological and biochemical analysis supported the differentiation of strain AS-0823(T) from S. longisporus JCM 4395(T). Therefore, strain AS-0823(T) represents a novel species, for which the name Streptomyces coacervatus sp. nov. is proposed. The type strain is AS-0823(T) ( = IFM 11055(T)  = DSM 41983(T)  = JCM 17138(T)).

Nocardia terpenica sp. nov., isolated from Japanese patients with nocardiosis

Two bacterial strains isolated from different hospitals in Japan were subjected to a polyphasic analysis. Strains IFM 0406 and IFM 0706T, producers of novel terpenoid antibiotics, were found to have morphological, biochemical, physiological and chemotaxonomic properties consistent with their classification in the genus Nocardia, except for the presence of MK-8(H4) as one of the predominant menaquinones in addition to the major menaquinone MK-8(H4ω-cyc). The 16S rRNA gene sequence similarity of strains IFM 0406 and IFM 0706T was 99.9 %, and the closest members of Nocardia to these strains were the type strains of Nocardia nova and Nocardia mexicana, showing similarity of 97.5 and 97.1 %, respectively. Based on their characteristic phenotypic and phylogenetic properties, a novel species of the genus Nocardia, Nocardia terpenica sp. nov. is proposed for the two strains. The type strain is IFM 0706T (=JCM 13033T=DSM 44935T=NBRC 100888T).

Nocardia acidivorans sp. nov., isolated from soil of the island of Stromboli

A Gram-positive, non-spore-forming bacterium (strain GW4-1778T) was isolated from soil of the Italian island of Stromboli. 16S rRNA gene sequence similarity studies showed that strain GW4-1778T is a member of the genus Nocardia, most closely related to Nocardia pseudobrasiliensis (GenBank accession no. DQ659914; 98.6 %), Nocardia nova (Z36930; 98.6 %), Nocardia niigatensis (AB092563; 98.4 %), Nocardia jiangxiensis (AY639902; 98.0 %), Nocardia uniformis (Z46752; 98.0 %) and Nocardia miyunensis (AY639901; 97.8 %). Strain GW4-1778T could be distinguished from any other established Nocardia species by sequence similarity values of less than 97.5 %. Strain GW4-1778T exhibited a quinone system with the predominant compound MK-8 (H4, ω-cycl) (99.5 %) and traces of MK-8 (H4), characteristic for the genus Nocardia. The polar lipid profile of strain GW4-1778T consisted of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides, a unknown polar lipid and trace amounts of two unknown lipids and the major fatty acids were C15 : 0, C16 : 0, C17 : 1 ω8c and 10-methyl C17 : 0. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW4-1778T from related species with 16S rRNA gene similarities of >97.5 %. Therefore, strain GW4-1778T merits species status, for which the name Nocardia acidivorans sp. nov. is proposed, with the type strain GW4-1778T (=CCUG 53410T=CIP 109315T=DSM 45049T).

Analysis of multiple differing copies of the 16S rRNA gene in five clinical isolates and three type strains of Nocardia species and implications for species assignment

Five clinical isolates of Nocardia that showed ambiguous bases within the variable region of the 16S rRNA gene sequence were evaluated for the presence of multiple copies of this gene. The type strains of three Nocardia species, Nocardia concava, Nocardia ignorata, and Nocardia yamanashiensis, which also showed ambiguous bases in the variable region, were also examined. Cloning experiments using an amplified region of the 16S rRNA that contains the variable region showed that each isolate possessed 16S rRNA genes with at least two different sequences. In addition, hybridization studies using a 16S rRNA gene-specific probe and extracted genomic DNA of the patient isolates and of the type strain of N. ignorata showed that each isolate possessed at least three copies of the gene. These multiple differing copies of the 16S rRNA gene and the results of DNA-DNA hybridization studies indicate problems of species definition and identification for such isolates. A broader species concept than that currently in vogue may be required to accommodate such organisms.

Taxonomy and Phylogenetic Analysis of Infectious Nocardia Strains Isolated from Clinical Samples

Following recent advances in medical technology, the increased number of immunocompromised patients such as those with organ transplants has led to an increase in opportunistic infections due to Nocardia. Although nocardiosis has been considered to be rare, recent reports indicate that the incidence of the infection is increasing. The Nocardia asteroides group is the principal source of infectious species, but the definition of species in Nocardia is problematic because species identification of N. asteroides has been based on mainly morphological and biochemical properties. Additionally, it was assumed that a clinical strain with properties that did not fully coincide with existing species was N. asteroides sensu lato. This caused problems in both clinical and taxonomical fields, and reclassification of N. asteroides sensu lato was necessary. Therefore, determination of the appropriate taxonomic position of N. asteroides sensu lato that is now classified as N. asteroides sensu stricto was conducted using a molecular phylogenetic method. From 1965 to 2001, twenty-two strains of N. asteroides sensu lato were isolated from clinical samples. The phylogenetic tree using 16S rDNA sequences and detailed biochemical characters on the 22 isolates was determined. Results revealed that nine strains should be reclassified into species other than N. asteroides sensu stricto, and we proposed nine new species of the genus Nocardia. In addition, we proposed eight other new species of the genus Nocardia from other samples; hence seventeen new species were proposed in total. We also reported the first infectious cases due to Nocardia beijingensis, Nocardia transvalensis and Nocardia pseudobrasiliensis in Japan.

Determination of antimicrobial susceptibility patterns of Nocardia spp. from clinical specimens by Etest

Susceptibilities to 11 antimicrobial agents were determined by Etest for 93 Nocardia isolates from clinical specimens and 15 type strains belonging to different Nocardia spp. All isolates were susceptible to trimethoprim-sulphamethoxazole, amikacin and linezolid, but susceptibilities of the various Nocardia spp. to beta-lactams, aminoglycosides, ciprofloxacin and clarithromycin varied markedly. Overall, there was a good correlation between the drug resistance patterns and the species identification established by conventional phenotypic tests and 16S rDNA sequencing. Among the different species encountered, Nocardia farcinica and Nocardia brasiliensis displayed the most multiresistant profiles, with resistance to imipenem occurring mainly among isolates of N. brasiliensis and Nocardia abscessus. The species variability in susceptibility profiles and the numerous recent taxonomic changes means that in-vitro susceptibility tests may be a complementary tool for the identification of Nocardia isolates from human clinical specimens. Further studies on a larger number of species from more diverse geographical sources, including species that are found less commonly among clinical isolates, are required to validate and extend the results.

Majority of Actinomadura clinical isolates from sputa or bronchoalveolar lavage fluid in Japan belongs to the cluster of Actinomadura cremea and Actinomadura nitritigenes, and the description of Actinomadura chibensis sp. nov

In Japan during 1996-2004, 21 actinomycete strains that have madurose as the diagnostic cell-wall sugar and show true branching in their substrate and aerial mycelia were isolated from sputa or bronchoalveolar lavage (BAL) fluid of patients with pulmonary infections or who were suspected of having related infections. Chemotaxonomic studies showed that all the isolates belong to the genus Actinomadura. Among them, six and seven strains were classified respectively into clusters of Actinomadura nitritigenes and Actinomadura cremea based on 16S rDNA analyses because their 16S rDNA similarities to those respective species were greater than 99.5%. To our knowledge, this is first report that strains of above two species were isolated from clinical specimens. Neither Actinomadura madurae nor Actinomadura pelletieri strain was isolated, and one new species, Actinomadura chibensis, was proposed; the remaining seven strains were not assigned into any known species, suggesting the presence of another new Actinomadura species.

Clinical and laboratory features of the Nocardia spp. based on current molecular taxonomy

The recent explosion of newly described species of Nocardia results from the impact in the last decade of newer molecular technology, including PCR restriction enzyme analysis and 16S rRNA sequencing. These molecular techniques have revolutionized the identification of the nocardiae by providing rapid and accurate identification of recognized nocardiae and, at the same time, revealing new species and a number of yet-to-be-described species. There are currently more than 30 species of nocardiae of human clinical significance, with the majority of isolates being N. nova complex, N. abscessus, N. transvalensis complex, N. farcinica, N. asteroides type VI (N. cyriacigeorgica), and N. brasiliensis. These species cause a wide variety of diseases and have variable drug susceptibilities. Accurate identification often requires referral to a reference laboratory with molecular capabilities, as many newer species are genetically distinct from established species yet have few or no distinguishing phenotypic characteristics. Correct identification is important in deciding the clinical relevance of a species and in the clinical management and treatment of patients with nocardial disease. This review characterizes the currently known pathogenic species of Nocardia, including clinical disease, drug susceptibility, and methods of identification.

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.

Nocardia jiangxiensis sp. nov. and Nocardia miyunensis sp. nov., isolated from acidic soils

The taxonomic positions of two soil actinomycetes, strains 117T and 43401T, provisionally assigned to the genus Nocardia were determined in a polyphasic study. The organisms were found to have phenotypic properties typical of members of the genus Nocardia, and formed a distinct branch in the Nocardia 16S rRNA gene tree. It was evident from the phylogenetic data that the isolates were most closely, albeit loosely, associated with the type strains of Nocardia nova and Nocardia pseudobrasiliensis. However, all four of these organisms were readily distinguishable from one another using DNA–DNA relatedness and phenotypic data. It is evident from the genotypic and phenotypic data that the two isolates should be recognized as novel species of the genus Nocardia. It is proposed, therefore, that strains 117T (=CGMCC 4.1904T=JCM 12860T) and 43401T (=CGMCC 4.1905T=JCM 12861T) be classified in the genus Nocardia as the type strains of Nocardia miyunensis sp. nov. and Nocardia jiangxiensis sp. nov., respectively.

Gordonia otitidis sp. nov., isolated from a patient with external otitis

The taxonomic positions of two clinically isolated actinomycetes were established using a polyphasic approach. The two strains, IFM 10032T, isolated from ear discharge of a 28-year-old Japanese female patient with external otitis, and IFM 10148, isolated from pleural fluid of a 60-year-old Japanese male patient with bronchitis, possessed meso-diaminopimelic acid as the diagnostic amino acid, MK-9(H2) as the predominant menaquinone and mycolic acids ranging from 58 to 64 carbons. The 16S rRNA gene sequences of the two strains were most closely related to those of Gordonia aichiensis, Gordonia sputi and ‘Gordonia jacobaea’. Differences in several phenotypic characteristics together with genotypic distinctiveness distinguish strains IFM 10032T and IFM 10148 from these three species. DNA–DNA hybridization results and the combination of genotypic and phenotypic data showed that the two strains belong to a single species, and merit recognition of a novel species within the genus Gordonia. The name proposed for this taxon is Gordonia otitidis sp. nov.; the type strain is IFM 10032T (=DSM 44809T=JCM 12355T=NBRC 100426T).

Nocardia concava sp. nov., isolated from Japanese patients

Two actinomycete strains, IFM 0354T and IFM 0576, isolated from Japanese patients, were found to have morphological, biochemical and chemotaxonomic properties consistent with their classification in the genus Nocardia. The strains resembled Nocardia otitidiscaviarum and Nocardia uniformis in their phenotypic properties. Comparative 16S rRNA gene sequence analysis showed that the strains are closely related to Nocardia seriolae. DNA–DNA relatedness values and phenotypic differences from N. seriolae indicated that the strains belong to a novel species of Nocardia, for which the name Nocardia concava sp. nov. is proposed. The type strain is IFM 0354T (=NBRC 100430T=JCM 12351T=DSM 44804T).

Distribution of nocardia species in clinical samples and their routine rapid identification in the laboratory

Eighty-six Nocardia strains isolated from clinical samples in Belgium were identified by 16S rRNA gene sequencing. Eighty-three (96%) strains belonged to only six Nocardia species: N. farcinica (38 [44%]), N. nova (19 [22%]), N. cyriacigeorgica (13 [15%]), N. brasiliensis (6 [6.9%]), N. abscessus (5 [5.8%]), and N. paucivorans (2 [2.3%]). A gallery of nine conventional and enzymatic tests was developed for the rapid identification of the most common species isolated during this survey. Pyrrolidonyl aminopeptidase, gamma-glutamyl aminopeptidase, alpha-mannosidase, and alpha-glucosidase were found to be highly discriminating and could be used to develop an identification scheme.

Nocardia polyresistens sp. nov

A novel actinomycete strain YIM 33361T was isolated from a soil sample collected from Yunnan, China. Comparative 16S rRNA gene sequencing showed that the strain constituted a distinct subclade within the genus Nocardia, displaying more than 3 % sequence divergence from established species. Based on its morphological, chemotaxonomic, phenotypic and genotypic characteristics, strain YIM 33361T (=CCTCC AA 204004T=KCTC 19027T) is proposed as the type strain of a novel species, Nocardia polyresistens sp. nov.

Nocardia xishanensis sp. nov., a novel actinomycete isolated from soil

The taxonomic position of a soil isolate, strain 276(T), was established using a polyphasic approach. The organism showed a range of chemical and morphological properties consistent with its classification in the genus Nocardia. An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genus Nocardia and related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the evolutionary radiation occupied by the genus Nocardia and was most closely related to the type strain of Nocardia abscessus. However, the two strains shared a low DNA-DNA relatedness value and were readily distinguished using a combination of phenotypic properties. The combined genotypic and phenotypic data show that strain 276(T) should be assigned to the genus Nocardia as a novel species. The name proposed for this new taxon is Nocardia xishanensis sp. nov. The type strain is 276(T) (=CGMCC 4.1860(T)=JCM 12160(T)).

Characterization of clinical isolates of pathogenic Nocardia strains and related actinomycetes in Thailand from 1996 to 2003

In Thailand from 1996 to 2003, 171 strains of pathogenic aerobic actinomycetes from clinical specimens were isolated. Of those strains, 134 were mycolic acid containing actinomycetes, including 96 strains of Nocardia species. Others included 10 strains of Gordonia, 14 strains of Rhodococcus, and 22 strains of Mycobacterium. One strain each of the genera Tsukamurella and Corynebacterium were also isolated. Also identified were 27 strains of non-mycolic acid containing actinomycetes. Our identification studies of 96 strains of Nocardia species showed that significant pathogens in Thailand were N. beijingensis (18 strains), N. cyriacigeorgica (13 strains), and N. farcinica (34 strains); the most prevalent species was N. farcinica (35.4%). We also isolated four strains of N. asiatica, five strains of N. asteroides sensu stricto, four strains of N. nova, seven strains of N. otitidiscaviarum, eight strains of N. transvalensis, and two strains of N. pseudobrasiliensis.

Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge

Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98.1-98.3 % similarity), Nocardia brasiliensis (97.9-98.0 %) and Nocardia tenerifensis (97.8-97.9 %). However, the results of DNA-DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.

Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated agar plate

A polyphasic study was undertaken to establish the taxonomic position of an actinomycete strain isolated from a contaminated agar plate. The strain, designated 7031T, had morphological and chemotaxonomic properties typical of the genus Nocardia. An almost-complete 16S rRNA gene sequence determined for the strain was aligned with available sequences for nocardiae, and phylogenetic trees were inferred using three tree-generating algorithms. Strain 7031T clustered with the type strains of Nocardia carnea and Nocardia flavorosea, showing low 16S rRNA gene sequence similarities to these species (97.2 and 97.5 %, respectively). The strain was also distinguished from the closest species by a range of phenotypic properties. It is proposed that the strain be recognized as a novel species of Nocardia, Nocardia pigrifrangens sp. nov., the type strain of which is 7031T (= AS 4.1808T = JCM 11884T).