Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil

Abstract Here, we report the draft genome sequence and annotation of Nocardia farcinica TRH1, a petroleum hydrocarbons degrading Actinobacteria isolated from the coastal water of Trindade Island, Brazil.

Clinical significance, antimicrobial susceptibility and molecular identification of Nocardia species isolated from children with cystic fibrosis

ABSTRACT Nocardia is an opportunistic pathogen that causes respiratory infections in immunocompromised patients. The aim of this study was to analyze the epidemiology, clinical significance and antimicrobial susceptibility of Nocardia species isolated from eight children with cystic fibrosis. The isolated species were identified as Nocardia farcinica, Nocardia transvalensis, Nocardia pneumoniae, Nocardia veterana and Nocardia wallacei. N. farcinica was isolated in three patients and all of them presented lung affectation with a chronic colonization and pneumonia. N. farcinica showed resistance against gentamicin, tobramycin, cefotaxime, but was susceptible to trimethoprim-sulfamethoxazole and amikacin. N. transvalensis, which was isolated from two patients, showed an association with chronic colonization. N. transvalensis was resistant to tobramycin and amikacin, but susceptible to ciprofloxacin, trimethoprim-sulfamethoxazole and cefotaxime. N. veterana, N. pneumoniae and N. wallacei were isolated from three different patients and appeared in transitory lung colonization. N. veterana and N. pneumoniae were susceptible to imipenem, trimethoprim-sulfamethoxazole, amikacin, tobramycin, and cefotaxime. N. wallacei was resistant to amikacin, tobramycin, imipenem, and trimethoprim-sulfamethoxazole and susceptible to ciprofloxacin and cefotaxime. All the isolates were identified up to species level by 16S rRNA gene sequencing. The presence of Nocardia in the sputum of patients with cystic fibrosis is not always an indication of an active infection; therefore, the need for a treatment should be evaluated on an individual basis. The detection of multidrug-resistant species needs molecular identification and susceptibility testing, and should be performed for all Nocardia infections.

Evaluation and enhancement of heavy metals bioremediation in aqueous solutions by Nocardiopsis sp. MORSY1948, and Nocardia sp. MORSY2014

ABSTRACT An analysis of wastewater samples collected from different industrial regions of Egypt demonstrated dangerously high levels of nickel (0.27-31.50 mg L-1), chromium (1.50-7.41 mg L-1) and zinc (1.91-9.74 mg L-1) in the effluents. Alarmingly, these heavy metals are among the most toxic knownones to humans and wildlife. Sixty-nine Actinomycete isolates derived from contaminated sites were evaluated under single, binary, and ternary systems for their biosorption capacity for Ni2+, Cr6+ and Zn2+ from aqueous solutions. The results of the study identified isolates MORSY1948 and MORSY2014 as the most active biosorbents. Phenotypic and chemotypic characterization along with molecular phylogenetic evidence confirmed that the two strains are members of the Nocardiopsis and Nocardia genera, respectively. The results also proved that for both the strains, heavy metal reduction was more efficient with dead rather than live biomass. The affinity of the dead biomass of MORSY1948 strain for Ni2+, Cr6+ and Zn2+ under the optimized pH conditions of 7, 8 and 7, respectively at 40 °C temperature with 0.3% biosorbent dosage was found to be as follows: Ni2+ (87.90%) > Zn2+ (84.15%) > Cr6+ (63.75%). However, the dead biomass of MORSY2014 strain under conditions of pH 8 and 50 °C temperature with 0.3% biosorbent dose exhibited the highest affinity which was as follows: Cr6+ (95.22%) > Ni2+ (93.53%) > Zn2+ (90.37%). All heavy metals under study were found to be removed from aqueous solutions in entirety when the sorbent dosage was increased to 0.4%.

MOLECULAR IDENTIFICATION AND ANTIMICROBIAL RESISTANCE PATTERN OF SEVEN CLINICAL ISOLATES OF Nocardia spp. IN BRAZIL / Identificação molecular e perfil de sensibilidade a antimicrobianos de sete isolados clínicos de Nocardia spp. no Brasil

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.

Nocardia é um microorganismo ubiquitário relacionado a infecções piogranulomatosas, com difícil resolução tecidual em humanos e animais. A doença é mundialmente emergente devido ao aumento de doenças e tratamentos imunossupressores. Este relato de casos ocorridos no Brasil visa apresentar a identificação molecular dos isolados e o padrão de sensibilidade a antimicrobianos por disco-difusão e concentração inibitória mínima (CIM) através de fitas E-test®. Os casos ocorreram em homens, em idade adulta. Três quadros foram cutâneos, dois pulmonares, um neurológico e um sistêmico. O quadro respiratório, o neurológico e um sistêmico estavam associados à doença ou terapia imunossupressoras. O sequenciamento do gene 16S rRNA (1491pb) possibilitou a identificação de quatro isolados de Nocardia farcinica, dois de Nocardia nova e um de Nocardia asiatica. N. farcinica foi observada em dois casos dermatológicos, um pulmonar e um quadro sistêmico, N. nova foi isolada de um caso neurológico e outro pulmonar; e N. asiatica em um caso dermatológico. O teste de disco-difusão mostrou que amicacina (100%), amoxicilina/clavulanato (100%), cefalexina (100%) e ceftiofur (100%) foram mais efetivos; enquanto gentamicina (43%), sulfametoxazol/trimetoprim (43%) e ampicilina (29%) foram menos efetivos. No entanto, no teste de concentração inibitória mínima (CIM), apenas um dos quatro isolados da espécie Nocardia farcinica mostrou-se resistente a sulfametoxazole-trimetropina.

Nocardia veterana: disseminated infection with urinary tract infection

Nocardia spp. are a group of aerobic actinomycetes widely distributed in soil, and associated with severe opportunistic infections, essentially pulmonary infections. We report the first case of disseminated infection associated with urinary tract infection caused by Nocardia veterana. The diagnosis was difficult; despite the presence of pulmonary nodules, the lung biopsies remained negative while only one aerobic blood culture and the urine culture were positive for N. veterana, identified after a 16S rDNA gene sequence analysis. Few cases of clinical importance due to N. veterana have been published since its characterization. The bacteriological diagnosis of nocardiosis can be difficult to establish because of the delayed growth and the specific techniques that are required. This case illustrates the necessity of performing specific investigations in immunocompromised patients who present with infectious disease because the severity of this infection requires early diagnosis and quick initiation of appropriate antibiotic therapy.

DIFFERENTIATION BETWEEN Nocardia spp. AND Mycobacterium spp.: CRITICAL ASPECTS FOR BACTERIOLOGICAL DIAGNOSIS / Diferenciação de Nocardia spp. e Mycobacterium spp.: aspectos críticos para o diagnóstico bacteriológico

New methodologies were developed for the identification of Nocardia but the initial diagnosis still requires a fast and accurate method, mainly due to the similarity to Mycobacterium, both clinical and bacteriologically. Growth on Löwenstein-Jensen (LJ) medium, presence of acid-fast bacilli through Ziehl-Neelsen staining, and colony morphology can be confusing aspects between Nocardia and Mycobacterium. This study describes the occurrence of Nocardia spp. in a mycobacterial-reference laboratory, observing the main difficulties in differentiating Nocardia spp. from Mycobacterium spp., and correlating isolates with nocardiosis cases. Laboratory records for the period between 2008 and 2012 were analyzed, and the isolates identified as Nocardia sp. or as non-acid-fast filamentous bacilli were selected. Epidemiological and bacteriological data were analyzed as well. Thirty-three isolates identified as Nocardia sp. and 22 as non-acid-fast bacilli were selected for this study, and represented 0.12% of isolates during the study period. The presumptive identification was based on macroscopic and microscopic morphology, resistance to lysozyme and restriction profiles using the PRA-hsp65 method. Nocardia spp. can grow on media for mycobacteria isolation (LJ and BBL MGIT™) and microscopy and colony morphology are very similar to some mycobacteria species. Seventeen patients (54.8%) were reported and treated for tuberculosis, but presented signs and symptoms of nocardiosis. It was concluded that the occurrence of Nocardia sp. during the study period was 0.12%. Isolates with characteristics of filamentous bacilli, forming aerial hyphae, with colonies that may be pigmented, rough and without the BstEII digestion pattern in PRA-hsp65 method are suggestive of Nocardia spp. For a mycobacterial routine laboratory, a flow for the presumptive identification of Nocardia is essential, allowing the use of more accurate techniques for the correct identification, proper treatment and better quality of life for patients.

Novas metodologias têm sido desenvolvidas para a identificação de Nocardia spp. mas o diagnóstico inicial ainda necessita de método rápido e preciso, principalmente devido à similaridade com o gênero Mycobacterium, clínica e bacteriologicamente. O crescimento em meio de Löwenstein Jensen (LJ), a presença de bacilos corados pela coloração de Ziehl Neelsen e colônias com características diferentes podem ser fatores de confusão entre nocardias e micobactérias. Este estudo descreve a ocorrência de Nocardia spp. em laboratório de referência em micobacteriologia, observando-se as principais dificuldades em diferenciar Nocardia spp. e Mycobacterium spp., correlacionando isolados com casos de nocardiose. Os registros laboratoriais dos anos 2008 a 2012 foram analisados e os isolados identificados como Nocardia sp. ou como bacilos não álcool - ácido resistentes (NBAAR) foram selecionados. Os dados epidemiológicos e bacteriológicos foram analisados. Trinta e três isolados identificados como Nocardia sp. e 22 como NBAAR foram selecionados para este estudo, perfazendo 0,12% do total de isolados identificados no período estudado. A identificação presuntiva foi baseada na morfologia macroscópica e microscópica, resistência à lisozima e perfis de restrição pelo método PRA-hsp65. Nocardia spp. pode crescer em meios de isolamento para micobactérias (LJ e BBL MGIT™) e microscopia de morfologia e as colônias são muito semelhantes a algumas espécies de micobactérias. Dezessete pacientes (54,8%) foram notificados e tratados para tuberculose, mas apresentaram sinais e sintomas para nocardiose. Concluimos que a ocorrência de Nocardia sp. no período estudado foi de 0,12%. Os isolados com características de bacilos filamentosos, formadores de hifas aéreas, com colônias que podem ter pigmento, rugosas e que não possuem padrão de digestão para BstEII no método PRA-hsp65 são sugestivos de Nocardia spp. Para um laboratório de rotina de Micobactérias, um fluxo de identificação presuntiva para Nocardia spp. é essencial para permitir que esses isolados sejam identificados com técnicas mais precisas, para que seja oferecido o tratamento adequado e qualidade de vida aos pacientes.

Long-term treatment of persistent disseminated Nocardia cyriacigeorgica infection

In this paper a disseminated persistent Nocardia cyriacigeorgica infection in an immunocompetent patient is described. The patient's long-term treatment, as well as its implications for managing similar cases in the future, is emphasized. Presenting with high fever, multiple nodules, and ulcerative cutaneous lesions of body sites, the patient was treated with various antimicrobials. Under combined therapy, empyema and arthritis, leading to disseminated nocardiosis, were seen. The overall treatment course was 28 months. It can be concluded that the choice of the antibiotics and optimal duration of treatment are uncertain; therefore the treatment of nocardiosis requires expertise.

Molecular identification and thermoresistance to boiling of Nocardia farcinica and Nocardia cyriacigeorgica from bovine bulk tank milk

Two strains of Nocardia spp. were isolated from bovine milk of two individual bulk tank. Molecular identification classified the strains as Nocardia farcinica and Nocardia cyriacigeorgica. The thermorresistance to boiling of the isolates was carried out and was observed bacterial growth after boiling. Our findings indicate the potential risk of pathogen transmission to humans through contaminated milk with Nocardia spp.

Management of post-operative Nocardia endophthalmitis.

Post-operative Nocardia endophthalmitis has an aggressive course and poor visual prognosis. It often masquerades as severe post-operative uveitis or toxic anterior segment syndrome due to the absence of vitreous involvement resulting in a delay in diagnosis. The poor prognosis in Nocardia endophthalmitis is due to severe intra-ocular inflammation which may lead to phthisis. Therefore, treatment with corticosteroids after appropriate antibiotics have been initiated may improve the outcome. This is an interventional case report highlighting the typical features of Nocardia endophthalmitis, which when diagnosed early and managed medically with antibiotics and steroids, resulted in an excellent visual outcome in our patient.

Infectious endocarditis caused by Nocardia sp.: histological morphology as a guide for the specific diagnosis

Nocardia is a rare opportunistic agent, which may affect immunocompromised individuals causing lung infections and exceptionally infective endocarditis (IE). There are few reports of IE caused by Nocardia sp., usually involving biological prostheses but rarely in natural valves. Its accurate microbiological identification may be hampered by the similarity with Rhodococcus equi and Corynebacterium spp. Here we report a case of native mitral valve IE caused by this agent in which the clinical absence of response to vancomycin and the suggestion of Nocardia sp. by histology pointed to the misdiagnosis of Corynebacterium spp. in blood cultures. The histological morphology can advise on the need for expansion of cultivation time and use of extra microbiological procedures that lead to the differential diagnosis with Corynebacterium spp. and other agents, which is essential to establish timely specific treatment, especially in immunocompromised patients.

Nocardia brasiliensis primary pulmonary nocardiosis with subcutaneous involvement in an immunocompetent patient.

This is a report of an unusual case of Nocardia brasiliensis causing primary pulmonary nocardiosis with disseminated subcutaneous lesions in an immunocompetent patient. This case highlights the importance of considering nocardiosis as a differential diagnosis in patients with pulmonary and cutaneous lesions and the need for vigorous management for complete cure.

Nocardiosis linfocutánea por Nocardia brasiliensis / Lymphocutaneous nocardiosis due to Nocardia brasiliensis

La nocardiosis linfocutánea es una de las formas clínicas de nocardiosis cutánea, producida en la mayoría de los casos por Nocardia brasiliensis. Puede ser difícil de diagnosticar sin una alta sospecha clínica, debido a su semejanza con otras enfermedades que pueden presentarse con patrones linfocutáneos. Los pacientes con nocardiosis cutánea tienen a menudo una historia previa de traumatismo cutáneo, ya sea herida punzante, picadura de insecto o abrasiones contaminadas. Se comunica un caso de nocardiosis linfocutánea primaria en una paciente inmunocompetente, de 33años.

Cavitary pneumonia caused by nocardia otitidiscaviarum

We report a case of cavitary pneumonia caused by N. otitidiscaviarum in a man with diabetes mellitus and thrombocytopenia treated with systemic corticosteroid. Taxonomic identification involved phenotypic testing and molecular identification that was carried out by DNA sequencing of the 16SrRNA gene.

Microbial degradation of sulfentrazone in a Brazilian rhodic hapludox soil

Sulfentrazone is amongst the most widely used herbicides for treating the main crops in the State of São Paulo, Brazil, but few studies are available on the biotransformation of this compound in Brazilian soils. Soil samples of Rhodic Hapludox soil were supplemented with sulfentrazone (0.7 µg active ingredient (a.i.) g-1 soil) and maintained at 27ºC. The soil moisture content was corrected to 30, 70 or 100 percent water holding capacity (WHC) and maintained constant until the end of the experimental period. Herbicide-free soil samples were used as controls. Another experiment was carried out using soil samples maintained at a constant moisture content of 70 percent WHC, supplemented or otherwise with the herbicide, and submitted to different temperatures of 15, 30 and 40º C. In both experiments, aliquots were removed after various incubation periods for the quantitative analysis of sulfentrazone residues by gas chromatography. Herbicide-degrading microorganisms were isolated and identified. After 120 days a significant effect on herbicide degradation was observed for the factor of temperature, degradation being higher at 30 and 40º C. A half-life of 91.6 days was estimated at 27º C and 70 percent WHC. The soil moisture content did not significantly affect sulfentrazone degradation and the microorganisms identified as potential sulfentrazone degraders were Nocardia brasiliensis and Penicillium sp. The present study enhanced the prospects for future studies on the bio-prospecting for microbial populations related to the degradation of sulfentrazone, and may also contribute to the development of strategies for the bioremediation of sulfentrazone-polluted soils.

occurrence of nocardia species among patients with pulmonary infection

The aim is to determine the frequency of Nocardia spp. among tuberculous patients in Khartoum state. Prospective study. Abu-Anga Teaching Hospital, El-Shaab Teaching Hospital and the Tuberculosis Reference Laboratory at the National Health Laboratory, Khartoum, Sudan. Three hundred and twenty-nine patients were included in this study during the period from October 2004 to January 2006. The patients were examined for the presence of acid-fast bacilli. Thin bacterial smears were prepared and stained by Ziehl Neelsen [ZN] stain. Two tubes of the Lowenstein-Jensen [LJ] medium were inoculated with 20 ul of the neutralized sputum sample that was obtained from the digestion and decontamination. One of the two tubes contained glycerol while the other tube contained pyruvic acid to isolate M. bovis species if encountered. All cultures were incubated at 37°C for 8 weeks. The growth was monitored up to the 8[th] week. Phenotypic characterization was performed by using different biochemical tests. Ten isolates showed rapid growth pattern within 2-3 days after inoculation. Further conventional methods suggested that all these isolates were belonging to the family Nocardiaceae. Nocardia spp revealed considerable occurrence among patients with pulmonary infections [3.3%]. This finding suggested that pulmonary nocardiosis might occur in patients who suffer from chronic lung disease in Sudan

Pulmonary nocardiosis due to nocardia farcinica in a renal transplant recipient.

Nocardia farcinica is an infrequent cause of nocardiosis among the renal transplant recipients and it has not been reported so far from India. We report a case of pulmonary nocardiosis due to N. farcinica in a 32-year-old woman with hypothyroidism and post-renal transplant status, currently on immunosuppressive therapy (prednisolone, azathioprine and tacrolimus). The N. farcinica isolate was susceptible to trimethoprim-sulfamethoxazole (TMP-SMZ), linezolid, imipenem, gentamicin but resistant to ceftriaxone, ciprofloxacin, tobramycin, erythromycin, amoxycillin-clavulanic acid and tetracycline. Treatment with TMP-SMZ and linezolid resulted in marked clinico-radiological improvement but after two weeks both of the drugs had to be stopped due to severe pancytopenia as adverse effect of their use. Currently, the patient is on imipenem and remains stable after four weeks of treatment. In N. farcinica infections, multi antibiotic resistance and toxicity of some specific drugs enhances the risk of therapeutic failure in renal transplant recipients.

Isolation of cryptococcus, candida, aspergillus, rhodotorula and nocardia from meningitis patients in Egypt

Meningitis occurs throughout Egypt and is largely attributed to bacterial pathogens, but there is little information on fungal etiologies of meningitis. We, therefore, investigated fungal infections among Egyptian patients with acute and subacute meningitis who tested negative for bacterial and viral agents. A total of 1000 cerebrospinal fluid [CSF] samples collected from nine governorates of Egypt during 1998-2002 were initially stained with Gram's, India ink, and lacto-phenol cotton-blue stains, and examined under light microscope to detect fungal elements. All CSF samples were cultured on brain heart infusion, Wickerham and Staib agar media for fungus isolation. CSF with suspected Cryptococcus neoforntans infections were also tested by latex agglutination test for antigen detection. Species identification of selected isolates was carried out at the Mycotic Diseases Branch, CDC, Atlanta, Georgia, USA. Fungal agents were detected microscopically and by culture in 17 of 1000 [1.7%] CSF samples tested. Ten of 17 were identified as C. neoformans var grubii [serotype A], 4 as Candida albicans, and one each of Aspergillus candidus, Rhodotorula mucilaginosa [rubra] and Nocardia spp [actinomycetes]. Out of the 17 cases with fungal CSF infection, 8 died [Cryptococcus-3. Candida-2, AspergiUus, Rhodotorula and Nocardia] and 2 suffered neurological sequelae. Of the 10 cryptococcal meningitis patients, 4 were HIV positive and one was diagnosed with lymphoma. To our knowledge, this is the first study on isolation of fungi other than Cryptococcus from CSF of Egyptian patients with acute/subacute meningitis. Consideration must now be given to cryptococcosis and candidiasis as potential etiologies of meningitis in Egypt

Nocardia brain abscess in a diabetic patient.

Brain abscess due to disseminated nocardia infection is an acute medical emergency among immunocompromised patients. We report a case of rapidly progressive nocardia brain abscess in an apparently healthy diabetic individual. The close similarity of the radiological features with those of malignancy and tuberculosis may delay the diagnosis of central nervous system (CNS) nocardiosis. A high index of suspicion and early intervention like stereotactic brain biopsy remain the cornerstone to increase the chance of positive clinical outcome.