Aerobic Actinomycetes Research Articles

Isolation and polyphasic characterization of aerobic actinomycetes genera and species rarely encountered in clinical specimens

The aim of this study was to identify aerobic actinomycetes strains belonging to genera and species rarely encountered in infections. Clinical specimens (sputum, gastric fluid and abscess pus) are collected from patients with symptoms of tuberculosis, pneumopathy, septicemy or having abscess, hospitalized in different services of infectious diseases in Constantine University Hospital Center, East of Algeria. A total of 49 strains of aerobic actinomycetes were isolated; among which 40 ones belong toStreptomyces, Nocardia and Actinomadura genera; however, nine strains are members of other actinomycetes genera, characterized in this study. Phenotypic, chemotaxonomic proprieties and sequencing 16S rRNA gene established identification of these isolates to:Nonomuraea roseola, Kribbella sp., Micromonospora aurantiaca, Nocardiopsissynnemataformans and Saccharothrix longispora. Identified isolates belonged to genera and species rarely encountered in clinical specimens; their role in pathology must be defined. Key words: Uncommon aerobic actinomycetes, clinical specimens, polyphasic taxonomy.

Draft Genome Sequence of the Lignocellulose Decomposer Thermobifida fusca Strain TM51

Here, we present the complete genome sequence of Thermobifida fusca strain TM51, which was isolated from the hot upper layer of a compost pile in Hungary. T. fusca TM51 is a thermotolerant, aerobic actinomycete with outstanding lignocellulose-decomposing activity.

Biodegradation of Clomazone in a California Rice Field Soil: Carbon Allocation and Community Effects

Degradation pathways for the herbicide clomazone in a California rice field soil were characterized via pulse-labeling of anaerobic (flooded) and aerobic (moist) soil microcosms. Clomazone-derived (13)C in the major C pools of a rice ecosystem and soil phospholipid fatty acid (PLFA) profiles were analyzed over time to determine if (1) the compound accumulates in the microbial biomass, (2) it affects temporal microbial population dynamics, and (3) it is either preferentially metabolized or cometabolized. In anaerobic microcosms, the compound was rapidly biotransformed to ring-open clomazone, upon which it persisted in the aqueous phase, whereas aerobic microcosms degraded it slower but a greater percentage was mineralized. Anaerobic biomass decreased after clomazone was added, and aerobic actinomycete abundance differed between treatments and controls. Additionally, PLFA and (13)C PLFA were statistically similar between treatment and controls. Thus, microbial cometabolism is likely to be the dominant degrading mechanism governing clomazone fate in California rice fields.

Characteristics of soil microbial community functional and structure diversity with coverage of Solidago Canadensis L

The relationship between Solidago canadensis L. invasion and soil microbial community diversity including functional and structure diversities was studied across the invasive gradients varying from 0 to 40%, 80%, and 100% coverage of Solidago canadensis L. using sole carbon source utilization profiles analyses, principle component analysis (PCA) and phospholipid fatty acids (PLFA) profiles analyses. The results show the characteristics of soil microbial community functional and structure diversity in invaded soils strongly changed by Solidago canadensis L. invasion. Solidago canadensis L. invasion tended to result in higher substrate richness, and functional diversity. As compared to the native and ecotones, average utilization of specific substrate guilds of soil microbe was the highest in Solidago canadensis L. monoculture. Soil microbial functional diversity in Solidago canadensis L. monoculture was distinctly separated from the native area and the ecotones. Aerobic bacteria, fungi and actinomycetes population significantly increased but anaerobic bacteria decreased in the soil with Solidago canadensis L. monoculture. The ratio of cy19:0 to 18:1ω7 gradually declined but mono/sat and fung/bact PLFAs increased when Solidago canadensis L. became more dominant. The microbial community composition clearly separated the native soil from the invaded soils by PCA analysis, especially 18:1ω7c, 16:1ω7t, 16:1ω5c and 18:2ω6, 9 were present in higher concentrations for exotic soil. In conclusion, Solidago canadensis L. invasion could create better soil conditions by improving soil microbial community structure and functional diversity, which in turn was more conducive to the growth of Solidago canadensis L.

NocardiaBrain Abscess Mimicking a Metastatic Brain Tumor: A Severe CNS Infection Requiring Aggressive Management

Nocardiosis is an uncommon Gram-positive bacterial infection caused by aerobic actinomycetes in the genus Nocardia. Nocardia spp. have the ability to cause localized or systemic suppurative disease in humans and animals. Nocardiosis is typically regarded as an opportunistic infection, but approximately one-third of infected patients are immunocompetent. We report a rare case of pulmonary nocardiosis and a brain abscess caused by Nocardia asteroides in an elderly woman with a history of Crohn’s disease. Radiographic imaging revealed a contrast-enhancing lesion with perilesional parenchymal edema that was preoperatively thought to be a neoplasm. The patient experienced aggressive disease progression simulating a metastatic brain tumor. Early diagnosis of norcadiosis, the absence of underlying disease, and the administration of appropriate antibiotics has a positive impact on prognosis. Familiarity with the magnetic resonance and computed tomography findings associated with CNS nocardiosis, such as those presented here, is essential for making an early diagnosis.

Multiple nocardial brain abscesses in an immunocompromised patient with myasthenia gravis

Introduction: Nocardia are gram positive, variably acid-fast positive diphtheroidlike to branched, filamentous, aerobic actinomycetes. Nocardiosis is an opportunistic infection that has been noted in patients with malignancies, systemic lupus erythematosus, HIV infection, hematopoietic stem cell transplant recipients and long-term steroid users. A 32- year-old female presented with history of myasthenia gravis on long-term glucocorticoid therapy. During her last admission, wound culture of her left shoulder abscess showed diptheroid organisms. Patient presented with severe headache, nausea, vomiting and altered mental status. She was initially diagnosed with metastatic cerebral abscess and treated with empiric antimicrobial therapy. Imaging study of the brain showed bilateral occipital ring enhancing lesions. Biopsy results came back as culture positive for nocardia. Patient was subsequently treated with intravenous antibiotics for a total of six months. Cases of nocardiosis may go undiagnosed, either because they respond to empiric antimicrobial treatment or because Nocardia spp. may be difficult to identify in cultures of clinical specimens. They may be mistaken for nonpathogenic microorganisms (diphtheroids) and discarded. High suspicion and early long term institution of therapy are key to a favorable outcome of this disease which has high mortality rates.

Pleuro-Pulmonary Nocardiosis as Opportunistic Infection in a Patient with Chronic Hepatitis C under Combination Treatment with Pegylated Interferon, Ribavirin, and Boceprevir.

Nocardiosis is an infrequent but serious pulmonary infection caused by Gram-positive aerobic actinomycetes. In this paper, we report on a 48-year-old patient with pleuropulmonary nocardiosis and cirrhosis due to chronic hepatitis C virus infection treated with triple antiviral treatment complicated by prolonged neutropenia.

Actinomycetoma in SE Asia: the first case from Laos and a review of the literature

BackgroundMycetoma is a chronic, localized, slowly progressing infection of the cutaneous and subcutaneous tissues caused either by fungi (eumycetoma or implantation mycosis) or by aerobic actinomycetes (actinomycetoma). It is acquired by traumatic implantation, most commonly in the tropics and subtropics, especially in rural agricultural communities. Although well recognized elsewhere in Asia, it has not been reported from the Lao People’s Democratic Republic (Laos).Case presentationA 30 year-old female elementary school teacher and rice farmer from northeast Laos was admitted to Mahosot Hospital, Vientiane, with a massive growth on her left foot, without a history of trauma. The swelling had progressed slowly but painlessly over 5 years and multiple draining sinuses had developed. Ten days before admission the foot had increased considerably in size and became very painful, with multiple sinuses and discharge, preventing her from walking. Gram stain and bacterial culture of tissue biopsies revealed a branching filamentous Gram-positive bacterium that was subsequently identified as Actinomadura madurae by 16S rRNA gene amplification and sequencing. She was treated with long-term co-trimoxazole and multiple 3-week cycles of amikacin with a good therapeutic response.ConclusionWe report the first patient with actinomycetoma from Laos. The disease should be considered in the differential diagnosis of chronic skin and bone infections in patients from rural SE Asia.

Antibiotic susceptibility patterns ofCrossiella equiandAmycolatopsisspecies causing nocardioform placentitis in horses

Nocardioform actinomycetes are significant causes of placentitis and abortions in horses. In the current study, antimicrobial susceptibility patterns of 38 Amycolatopsis spp. and 22 Crossiella equi isolates, the most common nocardioform actinomycetes causing placentitis in horses, were evaluated. Antimicrobial susceptibilities of these isolates were tested by broth microdilution method in a commercial system, which was designed for Nocardia spp., fast-growing Mycobacterium spp., and other aerobic actinomycetes. The minimum inhibitory concentration required to inhibit the growth of 90% of organisms (MIC(90)) of the following antibiotics tested for Amycolatopsis spp. were: 4 µg/ml for linezolid, trimethophrim-sulfametaxazole (TMP-SMX), and ciprofloxacin; 8 µg/ml for ceftriaxone, doxycycline, and minocycline; 16 µg/ml for amoxicillin-clavulanic acid, clarithromycin, and imipenem; >16 µg/ml for tobramycin; 32 µg/ml for amikacin and cefepime; and 128 µg/ml for cefoxitin. The MIC(90) levels for C. equi were 0.25 µg/ml for doxycycline; ≤1 µg/ml for minocycline; 2 µg/ml for linezolid and TMP-SMX; 4 µg/ml for ciprofloxacin; 8 µg/ml for amoxicillin-clavulanic acid, ceftriaxone, and imipenem; 16 µg/ml for clarithromycin; >16 µg/ml for tobramycin; 32 µg/ml for cefepime; >64 µg/ml for amikacin; and 128 µg/ml for cefoxitin.

Streptomyces oceani sp. nov., a new obligate marine actinomycete isolated from a deep-sea sample of seep authigenic carbonate nodule in South China Sea

A novel aerobic actinomycete strain, designated as SCSIO 02100(T), was isolated from a deep sea sediment sample collected from Northern South China Sea at a depth of 578 m. This isolate requires sea water or a sodium-supplemented medium for growth. BLAST searches based on the almost full length of the 16S rRNA gene sequence, showed that strain SCSIO 02100(T) had the highest similarities with Streptomyces armeniacus (JCM 3070(T)) (97.1 %). Phylogenetic trees reconstructed on the basis of 16S rRNA gene sequences revealed that strain SCSIO 02100(T) formed a distinct lineage with S. nanshensis SCSIO 01066(T) with 96.9 % similarity. Further analysis of the polyphasic taxonomic data, including morphological, phenotypic and chemotaxonomic properties, showed that strain SCSIO 02100(T) could be readily distinguished from the most closely related members of the genus Streptomyces. Thus, based on the polyphasic taxonomic data, a novel species, Streptomyces oceani sp. nov., is proposed, with the type strain SCSIO 02100(T) (=DSM 42043(T) = CGMCC 4.7007(T)).

Actinomycetoma and advances in its treatment

Actinomycetoma is a chronic subcutaneous infection caused by aerobic branching actinomycetes. Its clinical features are firm tumefaction of the affected site and the presence of abscesses, nodules, and sinuses that drain a seropurulent exudate containing filamenting granules. The disease is caused by inoculation of the infectious agent through minor trauma in susceptible individuals. Nocardia brasiliensis, Actinomadura madurae, and Streptomyces somaliensis are among the most frequent agents in the Americas. Cellular and humoral immunity have been studied in animal models. Standard therapy for uncomplicated cases is sulfamethoxazole-trimethoprim given for many months. Bone involvement, disseminated cases, and special locations require combined treatment with amikacin and sulfamethoxazole-trimethoprim. Isolated reports include the addition of other antibiotics such as rifampicin, imipenem, or meropenem. When needed, other aminoglycosides can be used. Amoxicillin-clavulanic acid is indicated in specific cases as alternative treatment. Oxazolidinone antibiotics, such as linezolid and other similar compounds (DA-7218 and DA-7157), have been studied in experimental infections in animal models as well as in vitro and ex vivo, with encouraging results.

Pseudonocardia antitumoralis sp. nov., a deoxynyboquinone-producing actinomycete isolated from a deep-sea sediment

An aerobic actinomycete, designated SCSIO 01299(T), was isolated from a deep-sea sediment collected from the northern South China Sea at a depth of 3258 m. The isolate was found to be a natural producer of the synthesized antitumour agent deoxynyboquinone and its three new derivatives, pseudonocardians A, B and C. A blast search based on almost-complete 16S rRNA gene sequences showed that strain SCSIO 01299(T) had high sequence similarities with members of the genus Pseudonocardia. The 16S rRNA gene sequence phylogenetic tree revealed that strain SCSIO 01299(T) was a member of the genus Pseudonocardia. Phenotypic analysis, chemotaxonomy and DNA-DNA relatedness could readily distinguish the isolate from established members in this genus. It was concluded that strain SCSIO 01299(T) represents a novel species, for which the name Pseudonocardia antitumoralis sp. nov. is proposed. The type strain is SCSIO 01299(T) ( = DSM 45322(T) = CCTCC M 2011255(T)).

DisseminatedNocardia farcinica: Literature Review and Fatal Outcome in an Immunocompetent Patient

Nocardia farcinica is a gram-positive, partially acid-fast, methenamine silver-positive aerobic actinomycete. Nocardia spp. are opportunistic pathogens, and N. farcinica is the least common species of clinical importance. Review of the recent literature and description of a immunocompetent patient with no known risk factors who contracted fatal N. farcinica sepsis. Positive pre-mortem and post-mortem cultures from the lung and synovium correlated with acute bronchopneumonia and synovitis at autopsy. Colonies of filamentous bacteria, which were not apparent in conventional hematoxylin and eosin-stained sections, were observed with gram and methenamine silver stains, but acid-fast stains were negative. A literature review revealed that disseminated N. farcinica often is associated with an underlying malignant tumor or autoimmune disease (88% of patients). Chemotherapy or corticosteroid treatments are additional risk factors. Trimethoprim-sulfamethoxazole typically is the first-line therapy for N. farcinica; treatment with amikacin and imipenem-cilastatin is used less often (7% of patients). Despite aggressive therapy, we observed that the death rate (39%) associated with N. farcinica in recent publications was eight percentage points higher than reported in a review from 2000.

Diversity and frequency of Nocardia spp. in the soil of Isfahan province, Iran

ObjectiveTo isolate and identify Nocardia spp. from soil in different regions of Isfahan province in the center of Iran. MethodsThis study was conducted in 32 districts (16 cities and 16 villages) in Isfahan province during two years. A total of 800 soil samples from these regions were studied by using kanamycin. The isolated Nocardia species were examined by gram and acid-fast staining and were identified biochemically and morphologically. The frequency and distribution of Nocardia spp. were determined in relation to different factors such as soil pH and temperate climate. ResultsFrom 153 (19.1%) Nocardia isolates identified, Nocardia asteroids (N. asteroids) complex (45.5%) and Nocardia brasiliensis (N. brasiliensis) (24.7%) were the most frequently isolated species, followed by Nocardia otitidiscaviarum (2.2%), Nocardiopsis dassonvillei, Actinomadura actinomadura (each 1.7%) and Nocardia transvalensis (1.1%) and also unknown spp. (23.0%). In this study, most species (54.4%) of Nocardia, especially N. asteroides complex were isolated from soils with pH: 7.01–8, whereas in pH: 8.01–9 more N. brasiliensis was isolated. The most Nocardia spp. was detected from regions with semi-nomadic and temperate climate (41.1%). ConclusionsN. asteroids complex is more prevalent in Isfahan province and soil can be a potential source of nocardiosis infections. It is to be considering that climate and soil pH are involved in the frequency and diversity of aerobic Actinomycetes.

Mechanism of H2S removal during landfill stabilization in waste biocover soil, an alterative landfill cover

Hydrogen sulfide (H2S) is one of the primary contributors to odors at landfills. The mechanism of waste biocover soil (WBS) for H2S removal was investigated in simulated landfill systems with the contrast experiment of a landfill cover soil (LCS). The H2S removal efficiency was higher than 90% regardless of the WBS or LCS covers. The input of landfill gas (LFG) could stimulate the growth of aerobic heterotrophic bacteria, actinomycete, sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) in the WBS cover, while that caused a decrease of 1–2 orders of magnitude in the populations of actinomycete and fungi in the bottom layer of the LCS cover. As H2S inputted, the sulfide content in the WBS cover increased and reached the maximum on day 30. In the LCS cover, the highest soil sulfide content was exhibited in the bottom layer during the whole experiment. After exposure to LFG, the lower pH value and higher sulfate content were observed in the top layer of the WBS cover, while there was not a significant difference in different layers of the LCS cover. The results indicated a more rapid biotransformation between sulfide and sulfate occurred in the WBS cover compared to the LCS.

Effect of Nigella sativa L. (black seed) extract on some clinically significant aerobic actinomycetes

The effect of extracts of Nigella sativa seeds against some clinically important actinomycetes namely: Gordonia, Mycobacterium, Nocardia and Rhodococcus were investigated. Petroleum ether extract of N. sativa seeds was found to be more effective than methanolic extracts. At 0.3 mg/ml, 0.5 cm inhibition zone was noticed in all test strains except Rhodococcus rhodochrous. Variable inhibition zones were shown by test strains to other concentrations used. The study concluded that petroleum ether extract of N. sativa is a promising candidate for further in vitrotesting and in vivo application as well. It is a recognized traditional healing and food additive seeds in many cultures with no reported harmful effect. Key words: Nigella sativa, actinomycetes, antibacterial agents.

A life-threatening case of disseminated nocardiosis due to Nocardia brasiliensis

Nocardiosis is a rare disease caused by infection with Nocardia species, aerobic actinomycetes with a worldwide distribution. A rare life-threatening disseminated Nocardia brasiliensis infection is described in an elderly, immunocompromised patient. Microorganism was recovered from bronchial secretions and dermal lesions, and was identified using molecular assays. Prompt, timely diagnosis and appropriate treatment ensured a favorable outcome.

A Case of Acquired Nocardia cyriacigeorgica from an intramuscular injection: Category: Clinical lesson

Nocardia is a genus of aerobic actinomycetes found ubiquitously in soil and aquatic habitats. It is a branching filamentous Gram positive bacillus. The taxonomy of Nocardia spp. has been revised using molecular techniques. Notably former members of the

Herbidospora mongoliensis sp. nov., isolated from soil, and reclassification of Herbidospora osyris and Streptosporangium claviforme as synonyms of Herbidospora cretacea

A Gram-reaction-positive aerobic actinomycete, designated strain MN08-A0118(T), which produced short chains of non-motile spores on the tips of long sporophores and formed yellow-brown colonies with branched substrate mycelium, was studied in detail to determine its taxonomic position. On the basis of 16S rRNA gene sequence analyses, strain MN08-A0118(T) was grouped into the genus Herbidospora, being most closely related to Streptosporangium claviforme (98.2%), Herbidospora osyris (98.2%), Herbidospora daliensis (98.2%), Herbidospora cretacea (97.9%) and Herbidospora yilanensis (97.4%). Chemotaxonomic data supported allocation of the strain to the genus Herbidospora. MK-10(H(4)) was the predominant menaquinone with minor amounts of MK-10(H(6)), MK-10(H(2)) and MK-9(H(4)); the fatty acid profile contained major amounts of iso-C(16:0), C(17:0) 10-methyl, iso-C(14:0) and iso-C(16:0) 2-OH; the phospholipid profile contained phosphatidylethanolamine, phosphatidylmethylethanolamine and glucosamine-containing phospholipids; and the whole-cell sugars included ribose, glucose, galactose, madurose and rhamnose (trace). The phylogenetic data, phenotypic and genotypic properties and DNA-DNA hybridization differentiated this strain from its closely related strains, S. claviforme (35-54% DNA-DNA relatedness), H. osyris (39-51%), H. daliensis (3-16%), H. cretacea (34-39%) and H. yilanensis (34-42%). Thus, MN08-A0118(T) represents a novel species of the genus Herbidospora, for which the name Herbidospora mongoliensis sp. nov. is proposed, with MN08-A0118(T) ( = NBRC 105882(T) = VTCC D9-22(T)) as the type strain. In addition, DNA-DNA hybridization results showed that S. claviforme and H. osyris are synonyms of H. cretacea.

Streptomyces panacagri sp. nov., isolated from soil of a ginseng field

A Gram-positive, spore-forming, aerobic actinomycete, strain Gsoil 519T, was isolated from soil of a ginseng field of Pocheon province in South Korea. The closest phylogenetic relatives were Streptomyces marinus Sp080513GE-26T (97.94 % 16S rRNA gene sequence similarity), Streptomyces albiaxialis NRRL B-24327T (97.84 %), Streptomyces albus subsp. albus DSM 40313T (97.84 %), Streptomyces almquistii NBRC 13015T (97.81 %), Streptomyces gibsonii NBRC 15415T (97.81 %), Streptomyces rangoonensis NBRC 13078T (97.81 %), Streptomyces sodiiphilus YIM 80305T (97.77 %) and Streptomyces flocculus NBRC 13041T (97.67 %). The G+C content of the genomic DNA was 71.8 mol%. The chemotaxonomic data [MK-9(H6) and MK-9(H8) as the major menaquinones; ll-diaminopimelic acid as a component of the cell-wall peptidoglycan; ribose, xylose, mannose and glucose as the major cell-wall sugars; and anteiso-C15:0, iso-C15:0, iso-C17:0, anteiso-C17:0 and C16:0 as the major fatty acids] supported the affiliation of strain Gsoil 519T to the genus Streptomyces. The physiological and biochemical characteristics and the low level of DNA-DNA relatedness differentiated the isolate genotypically and phenotypically from recognized members of the genus Streptomyces. The isolate, therefore, represents a novel species, for which the name Streptomyces panacagri sp. nov. is proposed, with Gsoil 519T (=KCTC 19139T=DSM 41871T) as the type strain.