Identification of nocardia species by restriction endonuclease analysis of an amplified portion of the 16S rRNA gene

Nocardia infections in cats: a retrospective multi-institutional study of 17 cases

OBJECTIVE

To record 17 cases of nocardiosis in cats from eastern Australia and to compare this series with cases previously reported.

DESIGN

Retrospective/prospective study.

RESULTS

Nocardia spp infections were diagnosed in 17 cats over 14 years from the three eastern states of Australia. There were no isolates from dogs during this period, but one isolate from a koala and two from dairy cows. The majority of cats presented with spreading lesions of the subcutis and skin associated with draining sinus tract(s). Early cutaneous lesions consisted of circumscribed abscesses. Infections spread at a variable rate, generally by extension to adjacent tissues. Lesions were generally located in regions subjected to cat bite or scratch injuries, including limbs, body wall, inguinal panniculus and nasal bridge. In some other cases, lesions were situated on distal extremities. The clinical course was variable, from chronic, indolent, initially localised infections to acute fulminating disease. Of the 17 cats, 14 were domestic crossbreds and three were purebreds. There was a preponderance of male cats (12 castrated, 1 entire young adult, 1 entire kitten). Nine of 17 cats were 10 years or older. Interestingly, the majority of infections were attributable to N nova. Immediate and/or predisposing causes could be identified in all cases, and included: renal transplantation [one cat]; chronic corticosteroid administration [three cats]; catabolic state following chylothorax surgery [one cat]; fight injuries [seven cats]; FIV infections [three of seven cats tested]. Of the 17 cats, three were apparently cured. Four were thought to be cured, but infection recurred after several months. Three cats responded partially but were euthanased, while another was improving when it died of unrelated complications. Two died despite treatment and two were euthanased without an attempt at therapy. For two cats there were either insufficient records or the patient was lost to follow up.

CONCLUSION

Nocardiosis is a rare, serious disease. Currently it is more common in cats than dogs. Nocardial panniculitis may be clinically indistinguishable from the syndrome caused by rapidly growing mycobacteria. Although the prognosis is guarded, patients with localised infections caused by N nova often respond to appropriate therapy. If definitive treatment is delayed because of misdiagnosis, the disease tends to become chronic, extensive and refractory. Insufficient duration of therapy leads to disease recurrence.

Molecular diagnosis of fatal Nocardia farcinica pneumonia in an HIV-negative patient

Nocardiosis is a rare and potentially life-threatening infection caused by several species of the Nocardia genus. Most cases occur in immunocompromised patients, and a delay in establishing the diagnosis is common due to the non-specific clinical presentations and the difficulty in cultivating Nocardia. Although the majority of pulmonary nocardiosis cases are caused by Nocardia asteroides, cases of human infection due to N. farcinica are increasingly diagnosed due to recent developments in taxonomy and diagnostic methods. N. farcinica is a separate species from N. asteroides and appears to be more virulent and resistant to antibiotics. Herein, we describe the case of a 65-year-old HIV-negative immunocompromised patient with a fulminant bilateral pulmonary nocardiosis while on empirical treatment with trimethoprim/sulfamethoxazole and imipenem. Post-mortem diagnosis of N. farcinica infection was performed by means of DNA amplification and sequencing of the 65-kDa bacterial heat shock protein.

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.

Disseminated nocardiosis due to Nocardia farcinica: diagnosis by thyroid abscess culture

A previously healthy 75-year-old white male dentist presented with a 6-month history of low-back pain treated with chronic steroid therapy had a Nocardia farcinica infection diagnosed by aspirate of thyroid abscess and six blood cultures. Despite the treatment with parenteral combination of trimethoprim/sulfamethoxazole, the patient failed to respond and died after two days of therapy. Autopsy revealed disseminated nocardiosis, involving lungs with pleural purulent exudate in both sides, heart, thyroid, kidneys, brain, bones, and lumbosacral soft tissue with destruction of L2-L4.

Molecular diagnosis of culture-negative cerebral nocardiosis due to Nocardia abscessus

We describe a case of culture-negative cerebral nocardiosis in a 34-year-old immunocompetent man who presented multiple cerebral abscesses. All bacteriologic cultures were negative. Nocardiosis was diagnosed by using a direct genus-specific 16S rDNA amplification method, and Nocardia abscessus was identified by hsp65 sequence analysis. The patient is alive and well on imipenem and doxycycline therapy, 14 months after onset.

Use of PCR-restriction enzyme pattern analysis and sequencing database for hsp65 gene-based identification of Nocardia species

Nocardia identification required laborious and time-consuming phenotypic and chemotaxonomic methods until molecular methods were developed in the mid-1990s. Here we reassessed the capacity of PCR-restriction enzyme pattern analysis (PRA) of the hsp65 gene to differentiate Nocardia species, including 36 new species. Our results confirm that hsp65 PRA must no longer be used for Nocardia species identification, as many species have the same restriction pattern. We then compared sequencing-based strategies using an hsp65 database and a 16S rRNA database and found that the hsp65 region contained sufficient polymorphisms for comprehensive Nocardia species identification.

Multiple copies of the 16S rRNA gene in Nocardia nova isolates and implications for sequence-based identification procedures

Molecular investigation of two Nocardia patient isolates showed unusual restriction fragment length polymorphism patterns with restriction endonuclease assays (REA) using an amplified portion of the 16S rRNA gene. Patterns typical of Nocardia nova were obtained with REA of an amplified portion of the 65-kDa heat shock protein gene. Subsequent sequence analysis of the 16S rRNA gene regions of these isolates showed the presence of ambiguous bases within an expected restriction endonuclease recognition site which were not able to be resolved on repeat testing. Cloning of amplified regions of the 16S rRNA genes and subsequent sequencing of the resulting clones from the two patient isolates showed three different 16S rRNA gene sequences which corresponded to sequences found in N. nova, a molecular variant of N. nova, and a previously undescribed sequence. Hybridization studies using a DNA probe corresponding to an 89-bp conserved region of the 16S rRNA gene confirmed the presence of at least two copies of the 16S rRNA gene in the N. nova type strain, in a patient isolate identical to the molecular variant of N. nova, and in the two other patient isolates. All isolates were found to belong to the species N. nova as determined by DNA-DNA hybridization. Because minimal variation has been found in the 16S rRNA gene sequences of different species of Nocardia, those laboratories employing molecular methods for identification of these species must be aware of the potential identification complications that may be caused by the presence of differing 16S rRNA genes in the same isolate.

Biochemical Identification and Molecular Characterization (PCR-RFLP) of Nocardia Isolates from Sputum

BACKGROUND

Nocardia identification has been based on biochemical and morphological characteristics. However, molecular biology techniques allow a better characterization of species and biotypes that are related to invasive diseases.

METHODS

Twelve isolates of Nocardia spp. were obtained from sputum of patients with tuberculosis under retreatment. Identification was done based on morphological characteristics, biochemical tests (casein, tyrosine, xanthine, gelatin, and urea) and molecular biology techniques (PCR-RFLP) using restriction enzymes MspI, HinfI, BsaHI, HaeIII and BstEII.

RESULTS

Biochemical tests identified the 12 isolates as Nocardia asteroides. PCR-RFLP technique identified nine isolates to species and biotype level: five as N. asteroides type II, two as N. asteroides type VI, and two as N. asteroides type I. The remaining three isolates were identified as follows: one to species level as N. farcinica and two at genus level as Nocardia sp.

CONCLUSIONS

Significant statistical differences between the use of traditional techniques and PCR-RFLP were not found at genus level, but there were important differences at species and biotype level. Biochemical tests identified correctly the actinomycete isolates as belonging to Nocardia genus, but at N. asteroides complex level were not able to discern among their different species. PCR-RFLP is a rapid, non-expensive, and reliable method that allows to discriminate the N. asteroides complex species, identifying biotypes related to invasive disease. Our results suggest that the hospital environment was not a contamination source.

Molecular identification of Capnocytophaga spp. via 16S rRNA PCR-restriction fragment length polymorphism analysis

Capnocytophaga spp. have been implicated as putative periodontal pathogens associated with various periodontal diseases. Although the genus is known to contain five human oral isolates, accurate identification to species level of these organisms recovered from subgingival plaque has been hampered by the lack of a reliable method. Hence, most studies to date have reported these isolates as Capnocytophaga spp. Previous attempts at identification were based on biochemical tests; however, the results were inconclusive. Considering the differing virulence features of the respective isolates, it is crucial to identify these isolates to species level. The universal and conservative nature of the 16S rRNA gene has provided an accurate method for bacterial identification. The aim of this study was to identify Capnocytophaga spp. via restriction enzyme analysis of this gene (16S rRNA PCR-restriction fragment length polymorphism). The results (backed up by 16S rRNA gene sequencing) showed that this method reliably identifies all named Capnocytophaga spp. to species level.

Identification of Mycobacterium species by secA1 sequences

We describe a novel molecular method for the differentiation and identification of 29 mycobacterial species. The target is the secA1 gene that codes for the essential protein SecA1, a key component of the major pathway of protein secretion across the cytoplasmic membrane. A 700-bp region of the secA1 gene was amplified and sequenced from 47 American Type Culture Collection strains of 29 Mycobacterium species as well as from 59 clinical isolates. Sequence variability in the amplified segment of the secA1 gene allowed the differentiation of all species except for the members of the Mycobacterium tuberculosis (MTB) complex, which had identical sequences. A range of 83.3 to 100% interspecies similarity was observed. All species could also be differentiated by their amino acid sequences as deduced from the sequenced region of the secA1 gene, with the exception of the MTB complex. Partial sequences of secA1 from clinical isolates belonging to nine frequently isolated species of mycobacteria revealed a very high intraspecies similarity at the DNA level (typically >99%; range, 96.0 to 100%); all clinical isolates were correctly identified. Comparison of the deduced 233-amino-acid sequences among clinical isolates of the same species showed between 99.6 and 100% similarity. To our knowledge, this is the first time a secretion-related gene has been used for the identification of the species within a bacterial genus.

Nocardia kruczakiae sp. nov., a pathogen in immunocompromised patients and a member of the "N. nova complex"

Molecular methodologies have become useful techniques for the identification of pathogenic Nocardia species and for the recognition of novel species that are capable of causing human disease. Two isolates recovered from immunocompromised patients were characterized as Nocardia nova by biochemical and susceptibility testing results. The restriction fragment length polymorphism (RFLP) patterns obtained by restriction endonuclease analysis (REA) of an amplified portion of the heat shock protein gene were identical to those obtained with the type strain of N. nova. REA of an amplified portion of the 16S rRNA gene showed RFLP patterns that were unlike those obtained for the type strain of N. nova but that were similar to those obtained for the type strains of N. africana and N. veterana. Subsequent sequencing of a portion of the 16S rRNA gene produced identical results for the two patient isolates. Sequence analysis of 1,352-bp portions of the 16S rRNA gene indicated that these isolates were 99.8% similar to the recently described species N. veterana but were only 99.3, 98.1, and 98.1% similar to the type strains of N. africana, N. nova, and N. vaccinii, respectively. DNA-DNA hybridization studies confirmed that the two patient isolates belonged to the same species but were not closely related to N. africana, N. nova, N. vaccinii, or N. veterana. The patient isolates have been designated N. kruczakiae sp. nov. Because N. africana, N. veterana, and the new species are not readily differentiated from N. nova by phenotypic methods alone, the designation "N. nova complex" can be used to designate isolates such as these that phenotypically resemble N. nova but that have not been definitively characterized by 16S rRNA gene sequencing or DNA-DNA hybridization.

Can whole genome analysis refine the taxonomy of the genus Rhodococcus?

The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.

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.

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.

Evaluation of RIDOM, MicroSeq, and Genbank services in the molecular identification of Nocardia species

The molecular identification of Nocardia species, when compared to phenotypic identification, has two primary advantages: rapid turn-around time and improved accuracy. The information content in the 5'-end of the 16S ribosomal RNA gene is sufficient for identification of most bacterial species. An evaluation was performed to demonstrate the quality of results provided by two specialized databases (RIDOM and MicroSeq 500 versions 1.1 and 1.4.3, library version 500-0125, respectively) and the more general GenBank database. In addition, these results were compared with phenotypic identifications. Partial 5'-16S rDNA sequences from 64 culture collection strains (DSM, CIP, JCM, and ATCC) were derived, in duplicate, independently in two laboratories. Furthermore, the sequences and the conventional identification results of 91 clinical Nocardia isolates were determined. With the exception of N. soli and N. cummidelens, all Nocardia type strains were distinguishable using 5'-16S rDNA sequencing. Assuming a normal distribution for the pairwise distances of all unique Nocardia sequences and choosing a reporting criterion of > or = 99.12% similarity for a "distinct species", a statistical error probability of 1.0% can be calculated. When the various databases were searched with the clinical isolate sequences RIDOM gave a perfect match in 71.4% of cases whereas MicroSeq yielded a perfect match in only 26.4%. The GenBank service gave a 100% similarity in 59.3% but in 70.4% of these cases the results obtained were not exclusive for a single Nocardia species. Conventional methods gave a correct identification in 59 cases, although most recent taxonomic changes were not taken into account. The RIDOM service (http://www.ridom-rdna.de/) is in the process of making available a comprehensive and high-quality database for bacterial identification purposes and provides excellent results for the majority of Nocardia isolates.

Application of sucrose-gradient centrifugation for selective isolation of Nocardia spp. from soil

AIMS

To devise and evaluate a method for selective isolation of the less abundant actinomycetes, Nocardia spp. in soil.

METHODS AND RESULTS

This newly developed method is based on differentiating Nocardia from other actinomycete taxa by centrifugation. A water suspension of air-dried soil is centrifuged through a gradient consisting of 10, 20, 30, 40 and 50% sucrose at 240 x g for 30 min. The 20% sucrose layer, which is enriched with Nocardia spp., is then diluted and plated on humic acid-vitamin agar supplemented with antibacterial agents. The proposed method consistently achieved selective isolation of Nocardia spp. in all 14 soil samples tested, which accounted for 5-89% of the total microbial population recovered. Tentative taxonomic characterization based on a restriction fragment length polymorphism (RFLP) analysis of the 16S ribosomal DNA suggested that many of the soil isolates could belong to N. asteroides, N. salmonicida or N. uniformis.

CONCLUSIONS

Differential centrifugation can successfully and efficiently isolate soil Nocardia populations that are suppressed by conventional dilution plating approaches.

SIGNIFICANCE AND IMPACT OF THE STUDY

The development and application of new methodologies with which to isolate less-explored actinomycete taxa is important for improving our knowledge about their taxonomy, ecology and industrial applications.

Chronic granulomatous pleuritis caused by nocardia: PCR based diagnosis by nocardial 16S rDNA in pathological specimens

Nocardiosis is an uncommon infection caused by the aerobic actinomycete nocardia. Identification of the pathogen is essential for the definitive diagnosis and for an effective treatment. This report describes a case of chronic granulomatous pleuritis caused by nocardia. A 59 year old Japanese man had a history of repeated pyothorax. Right pleural decortication and thoracic drainage were performed. Microbiological examinations of the drained fluid failed to identify a pathogen. Pathological examinations revealed Gram positive filamentous and branching bacilli in the granulomatous lesion of the pleura. Sequencing of the 971 bp 16S ribosomal DNA extracted and amplified from paraffin wax embedded sections identified the microorganism as Nocardia sp. IFM 0860. The patient received sulfamethoxazol/trimethoprim and minocycline. Although the presence of a brain abscess was disclosed by systemic examination, the clinical course has been favourable. In this patient, polymerase chain reaction analysis of 16S ribosomal DNA in pathological specimens was useful in making an accurate diagnosis of nocardiosis and in determining the appropriate treatment.

Nocardia veterana as a pathogen in North American patients

The molecular methodologies used in our laboratories have allowed us to define a group of Nocardia isolates from clinical samples which resemble the type strain of Nocardia veterana. Three patient isolates and the type strain of N. veterana gave identical and distinctive restriction fragment length polymorphisms (RFLPs) for an amplified portion of the 16S rRNA gene. These three isolates and the N. veterana type strain also gave identical RFLPs for an amplified portion of the 65-kDa heat shock protein gene, but this pattern was identical to that obtained for the Nocardia nova type strain. Sequence analysis of both a 1,359-bp region of the 16S rRNA gene and a 441-bp region of the heat shock protein gene of the patient isolates showed 100% identities with the same regions of the N. veterana type strain. DNA-DNA hybridization of the DNA of one of the patient isolates with the DNA of the N. veterana type strain showed a relative binding ratio of 82%, with 0% divergence, confirming that the isolate was N. veterana. Biochemical and susceptibility testing showed no significant differences among the patient isolates and the N. veterana type strain. Significantly, the results of antimicrobial susceptibility testing obtained for our isolates were similar to those obtained for N. nova, indicating that susceptibility testing alone cannot discriminate between these species. We present two case studies which show that N. veterana is a causative agent of pulmonary disease in immunocompromised patients residing in North America. We also describe difficulties encountered in using 16S rRNA gene sequences alone for discrimination of N. veterana from the related species Nocardia africana and N. nova because of the very high degree of 16S rRNA gene similarity among them.

Nocardia veterana isolated from ascitic fluid of a patient with human immunodeficiency virus infection

Nocardia veterana is a recently characterized species within the genus Nocardia, and only three human clinical isolates have been reported for this species. We describe a case of ascitic fluid infection in an immunocompromised patient due to N. veterana. To our knowledge, this is the first report of a Nocardia sp. strain from ascitic fluid and the fourth report of N. veterana isolated from human samples. Chemotaxonomic methods showed the strain to belong to the genus Nocardia, and identification to the species level was done by 16S ribosomal DNA gene sequencing. The antibiotic susceptibility profile of N. veterana is reported here for the second time. The strain was deposited in the Collection of the Pasteur Institute and in the Culture Collection of the University of Göteborg (CIP 107497 and CCUG 46576). The corresponding 16S ribosomal DNA gene sequence is available from the GenBank database under accession number AY149599. A phylogenetic analysis was conducted and showed that N. veterana was most closely related to the recently characterized species Nocardia africana rather than to Nocardia vaccinii, as previously reported.

Successful management of disseminated Nocardia transvalensis infection in a heart transplant recipient after development of sulfonamide resistance: case report and review

Nocardia transvalensis is a rarely reported cause of clinically significant disease, and, to our knowledge, has not been reported previously as a cause of infection in the cardiac transplant population. We report a case of N transvalensis new taxon-2 pulmonary infection that disseminated to the brain and skin in a cardiac transplant recipient despite adequate sulfonamide serum levels. Subsequent isolates were resistant to sulfonamides, and molecular ribotyping of the primary and subsequent isolates confirmed that these were the same N transvalensis new taxon-2 strain. The taxonomic and diagnostic considerations, as well as the clinical significance of anti-microbial-resistant nocardia, are reviewed and discussed herein.

Nocardia veterana, a new emerging pathogen

Nocardia veterana is a newly described species named after the veteran's hospital where it was first isolated. This initial type strain was not thought to be clinically significant. We describe three cases of pulmonary disease attributable to N. veterana: two cases in patients presenting with multiple pulmonary nodules in a setting of immunocompromise and one case of exacerbation of chronic pulmonary disease. The isolates were susceptible to ampicillin, imipenem, gentamicin, amikacin, and trimethoprim-sulfamethoxazole and had reduced susceptibilities to ceftriaxone, cefotaxime, minocycline, and ciprofloxacin. The MICs of amoxicillin-clavulanate were higher than that of ampicillin alone, and the bacteria produced a beta-lactamase detectable only after induction with clavulanic acid. Phenotypically, the isolates could not be characterized beyond the Nocardia genus level. All three isolates were definitively identified as N. veterana by PCR and sequencing of the 16S rRNA gene. On the basis of their susceptibility and restriction enzyme analysis profiles, our findings indicate that they could potentially be misidentified as N. nova. These cases illustrate the pathogenic potential of this newly described species and emphasize the importance of accurate identification of Nocardia isolates to the species level by integrated use of phenotypic and genotypic methods.

Inter- and intraspecies variations of the 16S-23S rDNA intergenic spacer region of various streptococcal species

The 16S-23S rDNA intergenic spacer regions (ISR) of different streptococcal species and subspecies were amplified with primers derived from the highly conserved flanking regions of the 16S rRNA and 23S rRNA genes. The single sized amplicons showed a uniform pattern for S. agalactiae, S. dysgalactiae subsp. dysgalactiae (serogroup C), S. dysgalactiae subsp. equisimilis (serogroup G), S. dysgalactiae subsp. dysgalactiae (serogroup L), S. canis, S. phocae, S. uberis, S. parauberis, S. pyogenes and S. equi subsp. equi, respectively. The amplicons of S. equi subsp. zooepidemicus, S. porcinus and S. suis appeared with 3, 5 and 3 different sizes, respectively. ISR of selected strains of each species or subspecies investigated were sequenced and multiple aligned. This allowed a separation of ISR into regions, with 7 regions for S. agalactiae, S. dysgalactiae subsp. dysgalactiae (serogroup C), S. dysgalactiae subsp. equisimilis (serogroup G), S. dysgalactiae subsp. dysgalactiae (serogroup L), S. canis, S. phocae, S. pyogenes and S. suis, 8 regions for S. uberis and S. parauberis and mostly 9 regions for S. equi subsp. equi, S. equi subsp. zooepidemicus and S. porcinus. Region 4, encoding the transfer RNA for alanine (tRNA(Ala)), was present and identical for all isolates investigated. The size and sequence of ISR appears to be a unique marker for streptococci of various species and subspecies and could be used for bacterial identification. In addition the size and sequence variations of ISR of S. equi subsp. zooepidemicus, S. porcinus and S. suis allows a molecular typing of isolates of these species possibly useful in epidemiological aspects.

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.

Nocardia africana isolated from a feline mycetoma

Nocardia africana was isolated from a subcutaneous nodule of a cat. The isolate developed orange, wrinkled colonies. The bacteria were rod shaped to coccoid (1 by 5 microm) and gram positive. Analysis of the 16S ribosomal DNAs of the isolate and a reference strain of N. africana showed 100% homology.

The first isolation of Nocardia veterana from a human mycetoma

The clinical isolates from biopsy specimen human subcutaneous nodule developed orange-colored and wrinkled colonies on Sabouraud's dextrose agar at 24 C for 2 weeks. The isolates were aerobic and gram-positive. The bacteria were rod-shaped to coccoid and 1 x 5 microm in size. The assimilation tests revealed that the clinical isolate was identical to a reference strain of Nocardia veterana. A nucleotide sequence analysis of the 16S ribosomal DNA from the isolate and a reference strain of N. veterana showed 99.8% similarity. All data are consistent with the conclusion that the isolate in this human case of mycetoma is N. veterana.

Expanded spectrum of Nocardia species causing clinical nocardiosis detected by molecular methods

Nocardia species isolated from seven patients with clinical infection were investigated by conventional biochemical methods and 16S rRNA gene sequencing. Three isolates were identified as recently described species (i.e., N. paucivorans, N. abscessus and N. veterana). We provide data on the epidemiology, clinical significance and antimicrobial susceptibility of these newly described Nocardia species.

Diagnosis of nocardiosis by polymerase chain reaction: an experimental study in mice

In this study, we have established a sensitive semi-nested polymerase chain reaction (PCR) for detection of Nocardia in clinical specimens by first amplifying a 422 bp DNA fragment from the groEL gene, followed by a second amplification of 342 bp DNA by targeting sequences internal to the first amplicon. The semi-nested PCR was evaluated in a murine model of nocardiosis for detection of Nocardia in blood and visceral organs. Healthy BALB/c mice were intravenously infected with 0.2 ml suspension of 2.9 x 10(5)/ml cfu of Nocardia asteroides and N. farcinica. Viable counts and seminested PCR were performed post-infection with samples of blood as well as lung, liver, spleen, kidney and brain at 5 minutes, 3 h, and then every 24 h for 3 days. Of the 20 blood samples tested, 15 (75%) were Nocardia positive by culture and 19 (95%) were positive by semi-nested PCR. Likewise, in case of N. asteroides infection, 46% organ samples were positive by culture and 58% by semi-nested PCR. The positivity of organ samples was higher with N. farcinica, 60% by culture and 72% by PCR, which may be attributed to its increased virulence as compared to N. asteroides. These results demonstrate that semi-nested PCR is a rapid and sensitive method for detection of Nocardia in blood and different visceral organs. The diagnostic application of this method provides an additional advantage over culture techniques, as PCR can also detect L-forms of Nocardia in clinical specimens, which otherwise fail to grow on routine isolation medium.

Identification of medically relevant Nocardia species with an abbreviated battery of tests

Identification of Nocardia to the species level is useful for predicting antimicrobial susceptibility patterns and defining the pathogenicity and geographic distribution of these organisms. We sought to develop an identification method which was accurate, timely, and employed tests which would be readily available in most clinical laboratories. We evaluated the API 20C AUX yeast identification system as well as several biochemical tests and Kirby-Bauer susceptibility patterns for the identification of 75 isolates encompassing the 8 medically relevant Nocardia species. There were few biochemical reactions that were sufficiently unique for species identification; of note, N. nova were positive for arylsulfatase, N. farcinica were positive for opacification of Middlebrook 7H11 agar, and N. brasiliensis and N. pseudobrasiliensis were the only species capable of liquefying gelatin. API 20C sugar assimilation patterns were unique for N. transvalensis, N. asteroides IV, and N. brevicatena. There was overlap among the assimilation patterns for the other species. Species-specific patterns of susceptibility to gentamicin, tobramycin, amikacin, and erythromycin were obtained for N. nova, N. farcinica, and N. brevicatena, while there was overlap among the susceptibility patterns for the other isolates. No single method could identify all Nocardia isolates to the species level; therefore, a combination of methods was necessary. An algorithm utilizing antibiotic susceptibility patterns, citrate utilization, acetamide utilization, and assimilation of inositol and adonitol accurately identified all isolates. The algorithm was expanded to include infrequent drug susceptibility patterns which have been reported in the literature but which were not seen in this study.

Pulmonary Nocardiosis

Pulmonary nocardiosis is an uncommon but serious infection that is increasingly found in immunosuppressed persons, especially transplant recipients and persons with AIDS. The Nocardia species are denizens of soil and decaying plants that gain entry to humans through inhalation or inoculation. Pulmonary nocardiosis typically presents as an acute to subacute necrotizing pneumonia, with a variable clinical picture. Metastatic infections of the brain and subcutaneous tissues are common complications. Most clinical laboratories can isolate these microorganisms, but final speciation may be a challenge and antimicrobial susceptibility testing is especially difficult because of the slow rate of growth of Nocardia species. Full identification of species and susceptibility testing is important because of the epidemiologic implications and the difficulties of successfully treating these infections in immunosuppressed patients. Sulfonamides, including trimethoprim-sulfamethoxazole, remain the most reliable antimicrobials. Many alternative agents are active against Nocardia in vitro, but clinical data are limited.

Nocardia africana sp. nov., a new pathogen isolated from patients with pulmonary infections

Eight actinomycete strains, isolated from 8 out of 400 sputum samples examined, taken from patients with pulmonary diseases at the Chest Unit of Khartoum Teaching Hospital in the Sudan, were provisionally assigned to the genus Nocardia according to morphological criteria. These isolates were studied further in order to establish their taxonomic status. They were found to have morphological and chemical properties typical of nocardiae and formed a monophyletic clade in the 16S ribosomal DNA tree together with Nocardia vaccinii. The strains showed a unique pattern of phenotypic properties that distinguished them from representatives of recognized Nocardia species, including Nocardia vaccinii. The strains were considered to merit species status and were designated Nocardia africana sp. nov. The findings of the present study are consistent with the view that pulmonary nocardiosis may occur in a substantial proportion of patients who exhibit chronic lung diseases in African countries. It is important, therefore, that clinicians in such countries consider this condition, especially when patients with respiratory infections fail to respond to antitubercular therapy.