The Complexities of Nocardia Taxonomy and Identification.

Nocardia species are a complex group of organisms considered to belong to the aerobic actinomycetes. Of the validly described species, many have been implicated as the cause of serious human infections, especially in immunocompromised patients. The genus has a complicated taxonomic history; this is especially true for Nocardia asteroides, the type species of the genus and previously the most frequently reported nocardial taxon from human specimens. We provide background on the current taxonomy of Nocardia, with a focus on clinically relevant species, and discuss the currently available methods used to accurately identify isolates to the species, complex, or group level.

Nocardial cerebral abscess associated with mycetoma, pneumonia, and membranoproliferative glomerulonephritis.

Nocardial brain abscesses remain a clinical challenge. We successfully treated a patient with nocardial brain abscess, mycetoma, pneumonia, and glomerulonephritis. Nocardial soft tissue involvement, mycetoma, is well known. However, the fact that actinomycetoma can metastasize may not be as well appreciated. The association between nocardiosis and glomerulonephritis should be better clarified.

Rapid identification of Nocardia farcinica clinical isolates by a PCR assay targeting a 314-base-pair species-specific DNA fragment.

Nocardia farcinica is the most clinically significant species within the Nocardia asteroides complex. Differentiation of N. farcinica from other members of N. asteroides complex is important because this species characteristically demonstrates resistance to several extended-spectrum antimicrobial agents. Traditional phenotypic characterization of this species is time- and labor-intensive and often leads to misidentification in the clinical microbiology laboratory. We previously observed a 409-bp product for all strains of N. farcinica by using randomly amplified polymorphic DNA analysis with the primer DKU49. In this investigation, the 409-bp fragment was sequenced and then used to design a specific primer pair, Nf1 (16-mer) and Nf2 (16-mer), complementary to the 409-bp fragment. PCR amplification of genomic DNA from 28 N. farcinica isolates with Nf1 and Nf2 generated a single intense 314-bp fragment. The specificity of the assay with these primers was verified, since there were no PCR amplification products observed from heterologous nocardial species (n = 59) or other related bacterial genera (n = 41). Restriction enzyme digestion using CfoI and direct sequencing of the 314-bp fragment further confirmed the specificity of the assay for N. farcinica. This highly sensitive and specific PCR assay provides a rapid (within 1 day of obtaining DNA) method for identification of this medically important emerging pathogen. Rapid diagnosis of N. farcinica infection may allow for earlier initiation of effective therapy, thus improving patient outcome.

Characterization of Nocardia asteroides isolates from different ecological habitats on the basis of repetitive extragenic palindromic-PCR fingerprinting.

Thirteen isolates of Nocardia asteroides from both soils and aquatic samples (lake and moat sediments, as well as scum from activated sludge), together with a type strain and two known clinical isolates of this species, were characterized by repetitive extragenic palindromic-PCR fingerprinting with the BOX-A1R primer. The resulting DNA fingerprint patterns proved to be strain specific, and cluster analysis distinguished the soil isolates, the aquatic isolates, and the known strains as being in separate groups.

Phylogeny of the genus Nocardia based on reassessed 16S rRNA gene sequences reveals underspeciation and division of strains classified as Nocardia asteroides into three established species and two unnamed taxons.

Conventional identification of Nocardia in the routine laboratory remains problematic due to a paucity of reliable phenotypic tests and due to the yet-unresolved taxonomy of strains classified as belonging to the species Nocardia asteroides, which comprises the type strain and isolates with drug pattern types II and VI. The 16S rRNA gene of 74 representative strains of the genus Nocardia, encompassing 25 established species, was sequenced in order to provide a molecular basis for accurate species identification and with the aim of reassessing the phylogeny of taxons assigned to the species N. asteroides. The result of this phylogenetic analysis confirms that the interspecies heterogeneity of closely related nocardial species can be considerably low (a sequence divergence of only 0.5% was found between N. paucivorans and N. brevicatena). We observed a sequence microheterogeneity (sequence divergence of fewer than five bases) in 8 of 11 species of which more than one strain in the species was studied. At least 10 taxons were found that merit description as new species. Strains previously classified as N. asteroides fell into five distinct phylogenetic groups: the type strain cluster (N. asteroides sensu strictu), N. abscessus, N. cyriacigeorgica, and two clusters closely related to N. carnea or N. flavorosea. The strains within the latter two groups probably represent new species, pending further genetic and phenotypic evaluation. Restricted phenotypic data revealed that N. abscessus, N. cyriacigeorgica, and the two Nocardia species taxons are equivalent to drug patterns I, VI, and II, respectively. In the future, these data will help in finding species-specific markers after adoption of a more precise nomenclature for isolates closely related to N. asteroides and unravel confusing phenotypic data obtained in the past for unresolved groups of strains that definitely belong to separate taxons from a phylogenetic point of view.

A study of the enzymatic profile of soil isolates of Nocardia asteroides.

In this study, using the API-ZYM system, we have reported the enzyme profile of 42 soil strains and 2 clinical strains of Nocardia asteroides isolated locally. Of the 19 enzymes tested, only 7 were demonstrable in over 90% of the soil isolates. These included alkaline phosphatase, esterase lipase, leucine arylamidase, acid phosphatase, phosphohydrolase, alpha-glucosidase and beta-glucosidase. In addition, beta-galactosidase activity was demonstrated in all the strains by the O-nitrophenyl-beta-D-galactopyranoside (ONPG) test. The enzymes which were not demonstrable in > 95% of the strains included valine arylamidase, cystine arylamidase, trypsin, chymotrypsin, alpha-galactosidase, beta-glucoronidase, N-acetyl-beta-glucosaminidase, alpha-mannosidase and alpha-fucosidase. With the exception of valine arylamidase, which was lacking in all but one isolate, the enzyme profiles of the soil isolates were comparable with the clinical isolates of N. asteroides reported in previous studies. The reasons for this difference in the two sets of isolates is not clear. The study reinforces the view that specific differences in the enzymatic profiles of Nocardia species could be used for their rapid identification. However, more extensive studies are needed to establish the reproducibility of this method. To the best of our knowledge, this is the first study of the enzymatic profile of soil isolates of N. asteroides originating from a single geographic region.

Investigation of a pseudo-outbreak of Nocardia asteroides infection by pulsed-field gel electrophoresis and randomly amplified polymorphic DNA PCR.

Molecular strain typing by pulsed-field gel electrophoresis and by randomly amplified polymorphic DNA analysis was used to investigate a cluster of four Nocardia asteroides isolates associated with the BACTEC 460 TB system. An instrument motor drive misalignment resulted in inadequate needle sterilization and cross-contamination of BACTEC vials. This pseudo-outbreak illustrates the importance of proper BACTEC 460 needle sterilization and maintenance and confirms the usefulness of molecular typing methods for epidemiologic investigations.

Ribotyping: a tool for taxonomy and identification of the Nocardia asteroides complex species.

Ribotyping has been evaluated as a taxonomic tool for studying bacteria belonging to the Nocardia asteroides complex. The probe used was obtained by PCR from DNA extracted from the type strain Nocardia asteroides ATCC 19247, a sequence that codes partly for 16S rRNA. Interpretation of hybridization after EcoRI restriction of total DNA of 21 strains of the N. asteroides complex allowed for the identification of only four different ribotypes: two related to N. asteroides sensu stricto, one related to N. farcinica and one related to N. nova. These results confirm the classification established by Tsukamura in 1982 (M. Tsukamura, Microbiol. Immunol. 26:1101-1119, 1982) as well as the heterogeneity of N. asteroides sensu stricto species. Ribotyping may also provide a major identification technique for the species belonging to the N. asteroides complex.

DNA amplification and restriction endonuclease analysis for differentiation of 12 species and taxa of Nocardia, including recognition of four new taxa within the Nocardia asteroides complex.

Nineteen reference and 156 clinical strains of the genus Nocardia belonging to 12 taxonomic groups were studied for restriction fragment length polymorphism (RFLP) by using an amplified 439-bp segment of the 65-kDa heat shock protein gene. Of 30 restriction endonucleases, digestion with MspI and then digestion with BsaHI produced RFLP band patterns which separated all 12 groups except N. asteroides type IV from 6 of 12 N. transvalensis isolates and N. carnea from the N. asteroides type VI isolates. Commonly encountered species such as N. nova, N. farcinica, N. brasiliensis sensu stricto, and N. otitidiscaviarum were easily separated. Each taxon resulted in a single RFLP band pattern that included > or = 96% of all biochemically grouped isolates for 9 of 12 taxa with MspI and for 8 of 12 taxa with BsaHI. With the use of both patterns, only 6 of 175 (3.4%) isolates failed to fit the biochemically defined group patterns. These studies provide the first evidence for the separate identities of four antibiogram-defined (but currently unnamed) groups within the N. asteroides complex (types I, II, IV, and VI) and the presence of two subgroups within N. transvalensis. They also provide genotypic evidence for the separate identities of N. nova and N. farcinica. The lack of BstEII recognition sites in amplicons obtained from nocardiae provides a simple and rapid method for the differentiation of nocardiae from mycobacteria. DNA amplification with RFLP analysis is the first rapid method that distinguishes all clinically significant taxa and recognized species within the genus Nocardia.

Pathogenic Nocardia isolated from clinical specimens including those of AIDS patients in Thailand.

Forty strains of nocardioform microorganisms were isolated as clinical specimens including several from AIDS patients in Thailand. Among them, 37 strains were found to belong to the genus Nocardia. Our identification studies revealed that most of the strains (25 strains) belong to the N. asteroides group, i.e., N. asteroides sensu stricto and N. farcinica. Three strains were identified as N. otitidiscaviarum and two strains N. brasiliensis. In addition, 7 strains of rare pathogenic N. transvalensis were also isolated.

PIP: Nocardia is an aerobic gram-positive and partly acid-fast bacterium that belongs to the pathogenic actinomycetes. Nocardia can cause both systemic and cutaneous diseases. Cutaneous nocardiosis is thought to be induced by various predisposing factors, the most common of which include corticosteroid therapy, immunosuppressive therapy, and hematological malignancy. In recent years cases of infection have been increasing coupled with the increased use of immunosuppressive agents and the number of AIDS patients. Characterization studies of pathogenic Nocardia isolated clinically in Thailand from 1990 to 1994 were reported. 40 strains of nocardioform microorganisms (Nocardia like actinomycetes with meso-DAP, arabinose, galactose, and mycolic acid) were isolated as clinical specimens including several from AIDS patients. All 40 strains were isolated from clinical specimens at seven hospitals in Bangkok using Sabouraud dextrose agar medium or Ogawa medium. The analysis of mycolic acid profiles on thin-layer chromatography (TLC) plate showed that one strain had the same Rf values as that of Mycobacterium sp. and the remaining 39 strains had similar Rf values to those of Nocardia, Rhodococcus, and Gordona spp. Studies on their menaquinone composition showed that among 39 isolates, 37 strains had MK-8H4 (cycl.) as predominant menaquinone. 2 strains had MK-8(H2) as a predominant menaquinone and both were identified as Rhodococcus spp. 25 strains were found to belong to the N. asteroides group and were further divided into respective species, i.e., 12 strains of N. asteroides in a strict sense and 13 strains of N. farcinica on the basis of Na-citrate utilization, susceptibility to antimicrobial and antitumor agent (tobramycin and 5-fluorouracil), and ability to grow at 45 degrees Celsius. Three strains of N. otitidiscaviarum and two strains of N. brasiliensis were also identified and the remaining seven strains were eventually identified as N. transvalensis. Results of the drug susceptibility pattern test of Nocardia isolates correlated well with those obtained by the traditional identification system. Among 37 cases, there were 10 HIV seropositive and 2 seronegative patients, and the remaining cases were unknown. Further epidemiological studies may be needed to determine a possible association between AIDS and nocardiosis.

Use of yeast killer system to identify species of the Nocardia asteroides complex.

We evaluated the ability of the yeast killer system to differentiate members belonging to the Nocardia asteroides complex (Nocardia asteroides, Nocardia farcinica, and Nocardia nova). Nocardia strains were selected randomly from clinical isolates. Type strains of each Nocardia species and recognized killer yeasts were taken from different collections. A clear area of inhibition surrounding the yeast cells demonstrated a positive killer effect on Nocardia spp. Two yeast strains, Pichia mrakii (K9) and Pichia lynferdii (K76), showed different killer activities against each Nocardia species. The group N. asteroides was identified as K9+ K76-, the group N. farcinica was identified as K9- K76-, and the group N. nova was identified as K9+ K76+. The three killer identifications correlated with specific taxonomic groups determined by using classical methods. The yeast killer system may be a useful means for identifying organisms within the N. asteroides complex.

Application of the API YeastIdent system in determining the enzymatic profiles of Nocardia asteroides isolates.

Glucose represses production of ammonium in many clinical isolates of Nocardia asteroides growing on bromcresolpurple casein glucose agar. Strains exhibiting this property are designated as group A, while group B represents isolates showing a high degree of proteolytic activity and a resulting rapid increase in pH. Twenty isolates of N. asteroides were characterized as group A or B. Enzymatic profiles obtained using the API YeastIdent system showed significant enzymatic variation between 12 group B and 8 group A isolates. Proteolytic enzymes which most varied in activity between groups were glycine aminopeptidase, histidine aminopeptidase and leucyl glycine aminopeptidase. As some of the N. asteroides isolates were isolated from asymptomatic patients, it is of interest to consider the possibility of one group being of low virulence while the other is more strongly associated with infection.

Opacification of Middlebrook agar as an aid in distinguishing Nocardia farcinica within the Nocardia asteroides complex.

Among 58 aerobic actinomycetes isolated from different sources and geographical locations, none of 23 Nocardia asteroides isolates, at 18 N. farcinica isolates, 1 of 5 N. otitidiscaviarum isolates, and 1 of 4 Rhodococcus species isolates opacified Middlebrook 7H10 medium. Within the N. asteroides complex, this characteristic, together with growth at 45 degrees C and resistance to each of erythromycin, cefotaxime, and tobramycin, provides a simple means of distinguishing N. farcinica from N. asteroides.