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 aobensis Sp. Nov., isolated from patients in Japan

Five clinical isolates, strains IFM 0137, 0372(T), 0496, 0556, and 0952, were provisionally assigned to the genus Nocardia based on morphological criteria. Nearly complete 16S rDNA sequences were determined for these strains. These data showed that they are most similar to that of Nocardia africana, Nocardia cerradoensis and Nocardia veterana. However, DNA-DNA relatedness data showed that the five strains were of a single species and were distinguishable from N. africana, N. cerradoensis and N. veterana. Therefore, these strains represent a new species within the genus Nocardia. The designation of these five strains is Nocardia aobensis sp. nov. The type strain is IFM 0372(T) (=NBRC 100429(T)=JCM 12352(T)=DSM 44805(T)).

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).

[Pneumonia induced by nocardia -- a case report]

We describe a case of lung manifestation of nocardiosis with upper lobe shrinking of the right lung in a 45 year old patient without evident signs of an immuno-compromising illness. The patient came to the hospital in a reduced general state of health with severe cough, red and brown sputum and exertional dyspnoea. X-ray pictures of the thorax showed inflammatory infiltration and shrinking of the upper left lobe of the right lung. Gram-positive, branching rods were detected in the patient's bronchial secretion with the microscope and in cultures. Nocoardia transvalensis was identified via polymerase chain reaction (PCR). The antibiotic therapy was planned according to the bacterial resistance pattern. Imipenem was administered for 5 weeks and Amikacin was added for 3 weeks in the 3 (rd) week of therapy. The patient left the hospital in a good general state of health. There was no relapse.

Nocardia mexicana sp. nov., a new pathogen isolated from human mycetomas

Three isolates collected from human mycetomas and showing an unusual brownish purple pigmentation on Bennett agar plates were analyzed by a polyphasic taxonomic approach, including morphological, biochemical, physiological, and chemotaxonomic properties coupled with genomic and phylogenetic analysis. It clearly appeared that these microorganisms were distinct from their closest phenotypic and genetic match, the most related species according to 16S rRNA gene sequence analysis being Nocardia pseudobrasiliensis. The data obtained indicated that the three clinical strains should be recognized as a new species for which the name Nocardia mexicana sp. nov. is proposed.

Nocardia alba sp.nov., a novel actinomycete strain isolated from soil in China

A novel actinomycete strain, designated YIM 30243T, was isolated from a soil sample in Yunnan Province, China. Based on the results of phenotypic and genotypic characteristics, strain YIM 30243T should be assigned to a new species of the genus Nocardia, for which the name Nocardia alba sp. nov. is proposed. The type strain is YIM 30243T (= CCTCC AA001030T = DSM 44684T).

Pneumonia involving Aspergillus and Rhizopus spp. after a near-drowning incident with subsequent Nocardia cyriacigeorgici and N. farcinica coinfection as a late complication

Reported here is the case of a 22-year-old man who developed pneumonia with unusual pathogens after a near-drowning incident. On day 7 following admission, Rhizopus spp. and Aspergillus fumigatus were cultured from the patient's bronchoalveolar lavage fluid. One week later, sputum cultures revealed N. cyriacigeorgici as well as N. farcinica. The patient recovered fully after prolonged therapy with liposomal amphotericin B, amikacin, meropenem and cotrimoxazole.

Cytokine production and lymphocyte proliferation in patients with Nocardia brasiliensis actinomycetoma

IFN-gamma, TNF-alpha, IL-4, IL-10 and IL-12 concentrations in the supernatant of peripheral blood mononuclear cell (PBMC) cultures and the in vitro proliferation of PBMC were studied in 25 patients with actinomycetoma caused by Nocardia brasiliensis and in 10 healthy controls from endemic zones. Cell cultures were stimulated by a N. brasiliensis crude cytoplasmic antigen (NB) and five semi-purified protein fractions (NB2, NB4, NB6, NB8, and NB10) separated by isoelectric. Phytohemagglutinin (PHA) and purified protein derivative (PPD) of Mycobacterium tuberculosis were used as control antigens. Skin tests were performed by injecting 0.1 ml of candidin and PPD intradermally (ID). Patients showed a poor response to tuberculin, while their response to candidin was more than two fold greater than that observed in the controls. Cell proliferation showed no statistically significant differences in either group. IFN-gamma production was higher in the healthy controls than in the patients, whereas TNF-alpha secretion was slightly higher in the patients' cultures. IL-4 was detected in the patients' cultures but not in the controls. IL-10 and IL-12 were present at low concentrations in both groups. These results suggest that patients with actinomycetoma show normal antigen recognition, but with low IFN-gamma production, and higher concentrations of IL-4, IL-10 and TNF-alpha in the patients' PBMC cultures, indicating that they probably have a Th2 type of immune response.

[Characterization of bacteria of the genera Mycobacterium, Rhodococcus and Nocardia isolated from environmental objects in the Republic of Daghestan]

The bacteriological study of specimens taken from environmental objects, biomaterials from animals and sputa from tuberculosis patients revealed the ubiquity of Mycobacterium, Nocardia and rhodococci obtained from different kinds of environment in the Republic of Daghestan. In the identification 83.6% out of the isolated atypical Mycobacterium cultures were classified with Ranion groups II and IV. Among Nocardia, the most widespread organisms were N. asteroides (62.7%) and among rhodococci, R. erithropolis (61.9%).

[Pulmonary infection with Nocardia species: a report of 10 cases]

OBJECTIVE

To investigate the clinical features of pulmonary nocardiosis.

PATIENTS AND METHODS

We retrospectively reviewed ten consecutive patients (5 men, 5 women; aged 25 to 80 years (average 49.3 years)) with confirmed bacteriological pulmonary nocardiosis from 1998 to 2003. Patients were divided into two groups: infected (8 patients) and isolated (2 patients).

RESULTS

All patients had predisposing factors and/or pulmonary disease. Six were immunosuppressed by steroid therapy with or without other immunosuppressive drugs. The overall survival rate among infected patients was 75.0% (6/8), but the survival rate of patients who were diagnosed speedily by a gram-stain procedure was 85.7% (6/7).

CONCLUSIONS

Although pulmonary nocardiosis is difficult to diagnose, prompt use of the gram-staining procedure and appropriate treatment appeared to improve survival. And new diagnostic method is desirable.

Primary Nocardia brasiliensis of the eyelid

PURPOSE

To report a rare case of lymphocutaneous Nocardia brasiliensis originating in the eyelid.

DESIGN

Observational case report.

METHODS

The clinical presentation, workup, and treatment of a case of lymphocutaneous Nocardia brasiliensis originating in the eyelid are presented.

RESULTS

The patient presented with a preseptal cellulitis from an abrasion of the eyelid that progressed to submandibular lymph node suppuration. Culture was performed, and a diagnosis of lymphocutaneous Nocardia brasiliensis was made.

CONCLUSION

Nocardia brasiliensis may cause a lymphocutaneous infection of the face and must be considered in the differential diagnosis of preseptal cellulitis.

Nocardia testaceus sp. nov. and Nocardia senatus sp. nov., isolated from patients in Japan

Two actinomycete strains isolated from sputum between 1999 and 2001 in Japan were provisionally assigned to the genus Nocardia based on morphological criteria. These isolates were further studied in order to determine their specific taxonomic status. Detailed chemotaxonomic characterization and 16S rDNA gene sequence analysis of these isolates also confirmed that they belong to the genus Nocardia. The 16S rDNA sequence data of the two strains showed that they are most similar to that of Nocardia carnea and Nocardia flavorosea. However, DNA-DNA relatedness data showed that the two strains could be distinguished from N. carnea and N. flavorosea and therefore represented two new species within the genus Nocardia. The designation of the two isolated strains are Nocardia testaceus for IFM 0937(T) (=JCM 12235(T), DSM 44765(T)) and Nocardia senatus for IFM 10088(T) (=JCM 12236(T), DSM 44766(T)).

Nocardia farcinica arthritis of the knee. A case report

Nocardia is a gram positive, aerobic branched actinomycete; it is an ubiquitous soil saprophyte. As an infecting agent it has been increasingly identified in humans, especially in immuno-suppressed hosts. Nocardia as a cause of septic arthritis is very unusual. The described genus was Nocardia asteroides in nearly all previously reported cases. We report an unusual case of spontaneous Nocardia farcinica septic arthritis of the left knee in a 68-year-old man, who was under systemic corticosteroids for chronic obstructive pulmonary disease. The diagnosis was rapidly made by Gram and acid-fast stains and later confirmed by culture. PCR was used to identify the subtype. The patient was treated successfully with sulphametaxazole-trimethoprim for six months. Our case re-emphasises, especially in the immuno-compromised patient, the importance of performing fungal and acid-fast bacilli cultures, besides the most common bacterial cultures for aerobic and anaerobic organisms, in order to identify less common organisms and to initiate early and adequate treatment.

[Nocardia endocarditis in a native mitral valve]

Nocardiosis is an opportunistic infection that usually arises in immunodepressed patients. Cases in immunocompetent patients are uncommon. We report a 53-year-old woman diagnosed as having Nocardia sp. endocarditis in a native mitral valve, which required valve replacement.

Nocardia arthritidis sp. nov., a new pathogen isolated from a patient with rheumatoid arthritis in Japan

Two different bacterial strains with different drug susceptibilities were isolated from the sputum and an inflammatory discharge from a swelling in the left thigh of a patient with rheumatoid arthritis. Both bacterial strains were provisionally assigned to the genus Nocardia on the basis of their morphological and chemotaxonomic characteristics and were further studied in order to establish their taxonomic status. One strain (IFM 10034) was identified as Nocardia farcinica on the basis of its physiological characteristics. The other strain, which was designated Nocardia sp. strain IFM 10035(T), revealed a unique pattern of phenotypic properties that distinguished it from other representatives of established Nocardia species. Comparative 16S rRNA gene sequence studies of Nocardia sp. strain IFM 10035(T) also showed that the bacterium was closely related to the species Nocardia beijingensis. Determination of DNA-DNA relatedness, however, indicated that Nocardia sp. strain IFM 10035(T) could be delineated from N. beijingensis. The genotypic and phenotypic data combined indicated that the bacterium merits description as a new Nocardia species. The name proposed for the new species is Nocardia arthritidis sp. nov., the type strain being IFM 10035(T) (NBRC 100137(T), JCM 12120(T), DSM44731(T)). The present study suggests that Nocardia infections can be caused by multiple species of the bacterium.

Sequence-based identification of aerobic actinomycetes

We investigated the utility of 500-bp 16S rRNA gene sequencing for identifying clinically significant species of aerobic actinomycetes. A total of 28 reference strains and 71 clinical isolates that included members of the genera Streptomyces, Gordonia, and Tsukamurella and 10 taxa of Nocardia were studied. Methods of nonsequencing analyses included growth and biochemical analysis, PCR-restriction enzyme analysis of the 439-bp Telenti fragment of the 65 hsp gene, susceptibility testing, and, for selected isolates, high-performance liquid chromatography. Many of the isolates were included in prior taxonomic studies. Sequencing of Nocardia species revealed that members of the group were generally most closely related to the American Type Culture Collection (ATCC) type strains. However, the sequences of Nocardia transvalensis, N. otitidiscaviarum, and N. nova isolates were highly variable; and it is likely that each of these species contains multiple species. We propose that these three species be designated complexes until they are more taxonomically defined. The sequences of several taxa did not match any recognized species. Among other aerobic actinomycetes, each group most closely resembled the associated reference strain, but with some divergence. The study demonstrates the ability of partial 16S rRNA gene sequencing to identify members of the aerobic actinomycetes, but the study also shows that a high degree of sequence divergence exists within many species and that many taxa within the Nocardia spp. are unnamed at present. A major unresolved issue is the type strain of N. asteroides, as the present one (ATCC 19247), chosen before the availability of molecular analysis, does not represent any of the common taxa associated with clinical nocardiosis.

Nocardia neocaledoniensis sp. nov., a novel actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil

The taxonomic position of an actinomycete isolated from a hypermagnesian ultramafic soil was examined using a polyphasic approach. The strain, designated SBH(R) OA6(T), was shown to have chemical and morphological properties typical of members of the genus Nocardia. The organism was most closely associated with Nocardia asteroides using 16S rRNA gene sequence data. It showed a distinctive set of phenotypic properties that distinguished it from representatives of all species with validly published names classified in the genus Nocardia. The combined genotypic and phenotypic data show that strain SBH(R) OA6(T) (=DSM 44717(T)=NCIMB 13955(T)) merits description as the type strain of a novel Nocardia species, Nocardia neocaledoniensis sp. nov.

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

Comparative 16S rDNA studies on six strains of actinomycete isolated from clinical specimens revealed that they belong to the genus Nocardia and are closely related to Nocardia seriolae, Nocardia otitidiscaviarum, Nocardia uniformis, Nocardia pseudobrasiliensis and Nocardia crassostreae. However, the novel organisms consistently formed a clade distinct from that of the five latter species. Determination of DNA-DNA relatedness indicated that these strains could be classified under three novel species. Based on their phenotypic and phylogenetic characters, three novel species of the genus Nocardia are established: Nocardia inohanensis sp. nov. for IFM 0092(T) (=NBRC 100128(T)=JCM 11891(T)=DSM 44667(T)), Nocardia yamanashiensis sp. nov. for IFM 0265(T) (=NBRC 100130(T)=JCM 11893(T)=DSM 44669(T)) and Nocardia niigatensis sp. nov. for IFM 0330(T) (=NBRC 100131(T)=JCM 11894(T)=DSM 44670(T)), IFM 0260, IFM 0636 and IFM 0833.

Nocardia tenerifensis sp. nov

A Gram-positive, non-spore-forming bacterium (GW39-1573(T)) was isolated from soil of the Spanish island of Tenerife. 16S rRNA gene sequence similarity studies showed that strain GW39-1573(T) belonged to the genus Nocardia and was most closely related to Nocardia brasiliensis (98.0 %), Nocardia beijingensis (97.3 %), Nocardia transvalensis (97.5 %), Nocardia asteroides (97.2 %) and Nocardia farcinica (97.0 %). Strain GW39-1573(T) could be distinguished from all other validly described Nocardia species by sequence similarity values of less than 97 %. Chemotaxonomic data [major menaquinone: MK-8(H(4, omega-cycl)); major polar lipids: diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unknown glycolipid and an unknown phospholipid; major fatty acids: C(16 : 0), C(18 : 1)omega9c and 10 methyl C(16 : 0)] and the presence of mycolic acids supported the affiliation of strain GW39-1573(T) to the genus NOCARDIA: The results of DNA-DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW39-1573(T) from those related species that showed 16S rRNA gene sequence similarity values of greater than 97 %. Strain GW39-1573(T) merits species status, and the name Nocardia tenerifensis is proposed with the type strain GW39-1573(T) (=DSM 44704(T)=CIP 107929(T)).

Nocardia beijingensis, is a pathogenic bacterium to humans: the first infectious cases in Thailand and Japan

Nocardia beijingensis, a recently established new species, is an isolate from soil in China. During our taxonomic studies on 450 nocardial clinical isolates in Thailand and Japan, 17 strains from Thailand and 1 strain from Japan were found to have a similar physiological characteristic to those of N. beijingensis, such as a drug susceptibility pattern to three antimicrobial agents. Our phylogenetic studies on these 18 strains by 16S rRNA gene sequence analysis confirmed that these strains belong to N. beijingensis species. Phylogenetically, these newly isolated N. beijingensis strains were found to be classified into two distinct clades: one is a Japanese clade and other is a Chinese clade, including a reference strain and 17 Thai strains. This is the first report of human infection due to N. beijingensis strains, and we propose that the bacterium be categorized as an opportunistic infectious group regardless of its original isolation from soil.

Nocardia farcinica - a significant cause of mastitis in goats in Sudan : short communication

Fifteen of 100 mastitic milk samples from goats suffering from mastitis were tentatively identified as members of the genus Nocardia on the basis of selected phenotypic and chemotaxonomic characteristics. Six of the 15 strains were confirmed as Nocardia farcinica by 16S rDNA gene sequencing and subsequent aligning with relevant actinomycetes found in electronic databases and 2 by other identification criteria. N. farcinica is a serious cause of mastitis with a significant prevalence (15%) among the examined goats. Efforts are needed to optimise and simplify isolation and identification methods.

Evaluation of partial 16S ribosomal DNA sequencing for identification of nocardia species by using the MicroSeq 500 system with an expanded database

Identification of clinically significant nocardiae to the species level is important in patient diagnosis and treatment. A study was performed to evaluate Nocardia species identification obtained by partial 16S ribosomal DNA (rDNA) sequencing by the MicroSeq 500 system with an expanded database. The expanded portion of the database was developed from partial 5' 16S rDNA sequences derived from 28 reference strains (from the American Type Culture Collection and the Japanese Collection of Microorganisms). The expanded MicroSeq 500 system was compared to (i). conventional identification obtained from a combination of growth characteristics with biochemical and drug susceptibility tests; (ii). molecular techniques involving restriction enzyme analysis (REA) of portions of the 16S rRNA and 65-kDa heat shock protein genes; and (iii). when necessary, sequencing of a 999-bp fragment of the 16S rRNA gene. An unknown isolate was identified as a particular species if the sequence obtained by partial 16S rDNA sequencing by the expanded MicroSeq 500 system was 99.0% similar to that of the reference strain. Ninety-four nocardiae representing 10 separate species were isolated from patient specimens and examined by using the three different methods. Sequencing of partial 16S rDNA by the expanded MicroSeq 500 system resulted in only 72% agreement with conventional methods for species identification and 90% agreement with the alternative molecular methods. Molecular methods for identification of Nocardia species provide more accurate and rapid results than the conventional methods using biochemical and susceptibility testing. With an expanded database, the MicroSeq 500 system for partial 16S rDNA was able to correctly identify the human pathogens N. brasiliensis, N. cyriacigeorgica, N. farcinica, N. nova, N. otitidiscaviarum, and N. veterana.