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

Exploring Nocardia's ecological spectrum and novel therapeutic frontiers through whole-genome sequencing: unraveling drug resistance and virulence factors

Nocardia farcinica is the leading pathogen responsible for nocardiosis, a life-threatening infection primarily affecting immunocompromised patients. In this study, the genomic sequence of a clinically isolated N. farcinica sample was sequenced. Subsequently, the assembled genome was annotated to identify antimicrobial resistance and virulence genes, as well as plasmid and prophages. The analysis of the entire genome size was 6,021,225 bp, with a GC content of 70.78% and consists of 103 contigs and N50 values of 292,531 bp. The genome analysis revealed the presence of several antimicrobial resistance genes, including RbpA, mtrA, FAR-1, blaFAR-1, blaFAR-1_1, and rox. In addition, virulence genes such as relA, icl, and mbtH were also detected. The present study signifies that N. farcinica genome is pivotal for the understanding of antimicrobial resistance and virulence genes is crucial for comprehending resistance mechanism, and developing effective strategies to combat bacterial infections effectively, especially adhesins and toxins. This study aids in identifying crucial drug targets for combating multidrug-resistant N. farcinica in the future.

Updated Review on Nocardia Species: 2006-2021

This review serves as an update to the previous Nocardia review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace. Jr., Clin Microbiol Rev 19:259-282, 2006, https://doi.org/10.1128/CMR.19.2.259-282.2006). Included is a discussion on the taxonomic expansion of the genus, current identification methods, and the impact of new technology (including matrix-assisted laser desorption ionization-time of flight [MALDI-TOF] and whole genome sequencing) on diagnosis and treatment. Clinical manifestations, the epidemiology, and geographic distribution are briefly discussed. An additional section on actinomycotic mycetoma is added to address this often-neglected disease.

Insights from the comparative genome analysis of natural rubber degrading Nocardia species

Nocardia are known to be a facultative human pathogen and can cause infection in immune compromised patients. Though the details research on the virulence factors of Nocardia are scanty but numerous genes that code such factors were reported from different species of Nocardia. Despite of the presence of several virulence factors, species of this genus have been shown to have role in remediation of many toxic and hazardous materials from the environment. In this study, genome sequences of rubber degrading Nocardia sp. BSTN01 and N.nova SH22a have been analyzed to locate the potential virulence genes. Also, the genomes of facultative pathogenic Nocardia like, N.africana, N. brasiliensis, N. kruczakiae, N. transvalensis and N. veterana have been analyzed to find the gene encoding latex clearing protein (Lcp), a rubber oxygenase enzyme of Gram-positive action bacteria. The study provides an insight about the potentiality of rubberdegrading Nocardia species to emerge as future human pathogens and also the probability of a serious concern if the studied facultative pathogens of Nocardia like N. africana, N. brasiliensis, N. kruczakiae, N. transvalensis and N. veterana are capable of degrading rubber, a regularly used material in clinics. Moreover, use of such possible pathogenic strains for their known role in bioremediation of rubber waste from the environment might be deleterious.

Nocardiosis from 1888 to 2017

The genus Nocardia is an aerobic bacterium, Gram-positive and catalase positive that is in Nocardiaceae family. This bacterium first described by Edmond Nocard in 1888 and is not in human commensal bacteria. To date, nocardiosis incidence is increasing due to increase population growth rate, increase in patients with immune disorder diseases and immunocompromised patients. We surveyed taxonomic position, isolation methods, phenotypic and molecular identification at the genus and species levels, antibiogram, treatment and epidemiology in the world from 1888 to 2017.

Successful Treatment of Disseminated Nocardiosis Caused by Nocardia veterana in a Dog

A 5‐year‐old male castrated Lhasa Apso cross was evaluated for a 1‐month history of inappetence, lethargy, gagging, and progressive right thoracic limb lameness. Synovial fluid analysis revealed nonseptic suppurative inflammation, and a diagnosis of immune‐mediated polyarthritis (IMPA) was made. After 3 months of treatment with prednisone and later cyclosporine, the dog developed multiple firm cutaneous and subcutaneous masses and a focal mass within the jejunum. Cultures of blood, urine, skin lesions, and the jejunal mass identified Nocardia veterana by matrix‐absorption laser desorption ionization‐time‐of‐flight mass spectrometry (MALDI‐TOF MS) and allowed for earlier identification of the organism compared to more traditional secA1 gene sequencing. Immunosuppressive drug treatment was discontinued, and the dog was treated for 3 months by administration of trimethoprim‐sulfamethoxazole (TMS). No recurrence of clinical signs was reported 1 year later. This case report highlights the clinical utility of MALDI‐TOF MS, particularly for the rapid identification of slow‐growing, fastidious organisms.

Identification and antimicrobial susceptibility of clinical Nocardia species in a tertiary hospital in China

OBJECTIVES

There is a lack of information on the activities of antimicrobial agents against Nocardia clinical isolates of specific species in China. The aim of this study was to determine the antibiotic susceptibility of 28 clinical isolates of Nocardia spp. isolated from Beijing Chao-Yang Hospital (Beijing, China).

METHODS

Molecular diagnosis of Nocardia spp. was performed using partial 16S rRNA and rpoB gene sequences. Antimicrobial susceptibility testing was performed by broth microdilution according to Clinical and Laboratory Standards Institute (CLSI) recommendations.

RESULTS

The species distribution was as follows: Nocardia cyriacigeorgica (n=13); Nocardia farcinica (n=6); Nocardia beijingensis (n=3); Nocardia abscessus (n=2); Nocardia wallacei (n=2); Nocardia otitidiscaviarum (n=1); and Nocardia nova (n=1). The susceptibility rates to trimethoprim/sulfamethoxazole (SXT), linezolid, amikacin, imipenem, tobramycin, ceftriaxone and cefotaxime were 100.0%, 100.0%, 92.9%, 75.0%, 67.9%, 67.9% and 64.3%, respectively, whilst the resistance rate both to ciprofloxacin and clarithromycin was 71.4%.

CONCLUSIONS

N. cyriacigeorgica was the most frequently isolated Nocardia spp. All clinical isolates showed low susceptibility to ciprofloxacin and clarithromycin and complete susceptibility both to SXT and linezolid, which can be considered the primary choice for the treatment of Nocardia infections in China.

In Vitro Comparison of Ertapenem, Meropenem, and Imipenem against Isolates of Rapidly Growing Mycobacteria and Nocardia by Use of Broth Microdilution and Etest

We compared the activities of the carbapenems ertapenem, meropenem, and imipenem against 180 isolates of rapidly growing mycobacteria (RGM) and 170 isolates of Nocardia using the Clinical and Laboratory Standards Institute (CLSI) guidelines. A subset of isolates was tested using the Etest. The rate of susceptibility to ertapenem and meropenem was limited and less than that to imipenem for the RGM. Analysis of major and minor discrepancies revealed that >90% of the isolates of Nocardia had higher MICs by the broth microdilution method than by Etest, in contrast to the lower broth microdilution MICs seen for >80% of the RGM. Imipenem remains the most active carbapenem against RGM, including Mycobacterium abscessus subsp. abscessus For Nocardia, imipenem was significantly more active only against Nocardia farcinica Although there may be utility in testing the activities of the newer carbapenems against Nocardia, their activities against the RGM should not be routinely tested. Testing by Etest is not recommended by the CLSI.

Traumatic endophthalmitis caused by Nocardia kruczakiae in a patient with traumatic eye injury

Background

We describe a case of traumatic ocular endophthalmitis caused by Nocardia kruczakiae after vegetable trauma in an immunocompetent child.

Findings

A 5-year-old boy suffered from a trauma with a palm tree leaflet. Two months later, he was diagnosed with traumatic infectious uveitis and intumescent cataract with anterior capsule rupture. Intensive treatment with systemic and topical vancomycin, ceftazidime and methylprednisolone began. After 1 month, he underwent phacoemulsification with intraocular lens implantation (IOL).

After some episodes of reactivation, he was diagnosed with traumatic nocardial endophthalmitis from aqueous humour samples. Several operations and specific antibiotic therapy resolved the infection.

Conclusions

In cases of traumatic endophthalmitis and several recurrences, it is extremely useful to make an etiologic diagnosis in order to treat the patient with specific antibiotics.

Nocardia exalbida blebitis: a case report

PURPOSE

To report the first documented case of Nocardia exalbida blebitis.

METHODS

A 57-year-old immunocompetent African American man with a long-standing history of open-angle glaucoma in both eyes treated with trabeculectomy presented with a diffusely hyperemic, thin, cystic, leaky bleb with no discharge in his left eye. The patient underwent bleb revision using an amniotic membrane patch graft followed by 1 month of antibiotics. He presented second time with an inflamed eye and brisk leakage and underwent a second bleb revision. His cultures remained negative. Two months after this second surgery, an anterior staphyloma had formed within the bleb area, and visible leakage of purulent material and a dense hypopyon was noted. Gram stain of the material showed rare long-branching rods. The material was sent to an outside laboratory for culture and identification.

RESULTS

All 6 cultures were positive for N. abscessus complex and N. exalbida. The patient underwent 6 months of Bactrim therapy with topical sulfonamide and amikacin, leading to the disappearance of the hypopyon and an inflammation-free eye.

CONCLUSIONS

N. exalbida is a newly identified Nocardia species that must be considered as a possible infectious agent in immunocompetent patients with blebitis refractive to initial topical antibiotic therapy. Delay in diagnosis and initiation of appropriate antibiotic regimen can result in an aggressive inflammatory process and vision loss.

Creation of an In-House Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Corynebacterineae Database Overcomes Difficulties in Identification of Nocardia farcinica Clinical Isolates

Nocardiosis is a rare disease that is caused by Gram-positive actinobacteria of the Nocardia genus and affects predominantly immunocompromised patients. In its disseminated form, it has a predilection for the central nervous system and is associated with high mortality rates. Therefore, prompt identification of the pathogen is critical. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a relatively novel technique used for identification of microorganisms. In this work, an upgraded MALDI-TOF Biotyper database containing Corynebacterineae representatives of strains deposited in the Polish Collection of Microorganisms was created and used for identification of the strain isolated from a nocardial brain abscess, mimicking a brain tumor, in an immunocompetent patient. Testing with the API Coryne system initially incorrectly identified Rhodococcus sp., while chemotaxonomic tests, especially mycolic acid analysis, enabled correct Nocardia identification only at the genus level. Subsequent sequence analysis of 16S rRNA and secA1 genes confirmed the identification. To improve the accuracy of the results, an in-house database was constructed using optimized parameters; with the use of the database, the strain was eventually identified as Nocardia farcinica. Clinical laboratories processing various clinical strains can upgrade a commercial database to improve and to accelerate the results obtained. This is especially important in the case of Nocardia, for which valid microbial diagnosis remains challenging; reference laboratories are often required to identify and to survey these rare actinobacteria.

Identification of Nocardia species using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry

BACKGROUND

The MALDI (matrix-assisted laser desorption/ionization) Biotyper system for bacterial identification has already been utilized in clinical microbiology laboratories as a successful clinical application of protoemics. However, in cases of Nocardia, mass spectra suitable for MALDI Biotyper identification are often not obtained if such specimens are processed like general bacteria. This problem is related to the insufficiencies in bacterial spectrum databases that preclude accurate specimen identification. Here, we developed a bacterial processing method to improve mass spectra from specimens of the genus Nocardia. In addition, with the new processing method, we constructed a novel in-house bacterial database that combines a commercial database and mass spectra of Nocardia strains from the Department of Clinical Laboratory at Chiba University Hospital (DCLC) and the Medical Mycology Research Center at Chiba University (MMRC).

RESULTS

The newly developed method (Nocardia Extraction Method at DCLC [NECLC]) based on ethanol-formic acid extraction (EFAE) improved mass spectra obtained from Nocardia specimens. The Nocardia in-house database at Chiba University Hospital (NDCUH) was then successfully validated. In brief, prior to introduction of the NECLC and NDCUH, 10 of 64 (15.6%) clinical isolates were identified at the species level and 16 isolates (25.0%) could only be identified at the genus level. In contrast, after the introduction, 58 isolates (90.6%) were identified at the species level and 6 isolates (9.4%) were identified at the genus level.

CONCLUSIONS

The results of this study suggest that MALDI-TOF (time-of-flight) Biotyper system can identify Nocardia accurately in a short time in combination with a simple processing method and an in-house database.

Nocardiosis in 132 patients with cancer: microbiological and clinical analyses

OBJECTIVES

To correlate the microbiological and clinical features of infections caused by Nocardia species.

METHODS

We determined the species and drug susceptibility of 138 Nocardia strains isolated from 132 patients at the University of Texas M. D. Anderson Cancer Center (Houston, TX) from 2002 through 2012 and analyzed the clinical features.

RESULTS

The 132 patients included 82 men and 50 women with a mean age of 59.1 years. All except two had underlying cancer, and 47 (35.6%) also received a stem cell transplant. These patients experienced 136 episodes of Nocardia infection, including pulmonary infection, abscess of deep skin and soft tissue, bacteremia and dissemination, and brain abscess. The 138 Nocardia strains involved 27 species, of which 20 species have been described since 2000. Common species included Nocardia nova, Nocardia cyriacigeorgica, Nocardia farcinica, and Nocardia abscessus, together accounting for 59.4%. N nova caused most bacteremia cases, whereas N farcinica caused most of the skin and brain infections. Infections with a few recent species likely represented first confirmation or report of human infections. Antimicrobial susceptibility tests of 117 strains showed that they were all susceptible to trimethoprim-sulfamethoxazole and linezolid but variably susceptible to other drugs depending on species. Most patients who were treated for the infection showed improvement or resolution.

CONCLUSIONS

Diverse Nocardia species can cause secondary infections in patients with cancer. Timely species identification and antimicrobial susceptibility tests may guide treatment.

Identification, typing, and phylogenetic relationships of the main clinical Nocardia species in spain according to their gyrB and rpoB genes

This study compares the identification, typing, and phylogenetic relationships of the most prevalent clinical Nocardia species in Spain, as determined via sequence analysis of their housekeeping genes gyrB and rpoB, with the results returned by the gold standard 16S rRNA method. gyrB and rpoB analyses identified Nocardia abscessus, N. cyriacigeorgica, N. farcinica, and the N. nova complex, species that together account for more than half of the human nocardiosis cases recorded in Spain. The individual discriminatory power of gyrB and rpoB with respect to intraspecies typing, calculated using the Hunter-Gaston discriminatory index (HGDI), was generally high (HGDI, 0.85 to 1), except for rpoB with respect to N. farcinica (HGDI, 0.71). Phylogenetically, different degrees of intra- and interspecies microheterogeneity were observed for gyrB and rpoB in a group of 119 clinical strains. A single 16S haplotype was obtained for each species, except for the N. nova complex (8 types), while gyrB and rpoB were more polymorphic: N. abscessus had 14 and 18 haplotypes, N. cyriacigeorgica had 17 and 12, N. farcinica had 11 and 5, and the N. nova complex had 26 and 29 haplotypes, respectively. A diversity gradient was therefore seen, with N. farcinica at the bottom followed by N. abscessus and N. cyriacigeorgica in the middle and N. nova complex at the top. The complexity of the N. nova complex is highlighted by its six variations in the GyrB (126)AAAPEH motif. gyrB sequencing (with or without rpoB sequencing) offers a simple means for identifying the most prevalent Nocardia species in Spanish medical laboratories and for determining the intraspecific diversity among their strains.

Nocardia aciditolerans sp. nov., isolated from a spruce forest soil

Actinomycetes growing on acidified starch-casein agar seeded with suspensions of litter and mineral soil from a spruce forest were provisionally assigned to the genus Nocardia based upon colonial properties. Representative isolates were found to grow optimally at pH 5.5, have chemotaxonomic and morphological features consistent with their assignment to the genus Nocardia and formed two closely related subclades in the Nocardia 16S rRNA gene tree. DNA:DNA relatedness assays showed that representatives of the subclades belong to a single genomic species. The isolates were distantly associated with their nearest phylogenetic neighbour, the type strain of Nocardia kruczakiae, and were distinguished readily from the latter based on phenotypic properties. On the basis of these data it is proposed that the isolates merit recognition as a new species, Nocardia aciditolerans sp. nov. The type strain is isolate CSCA68(T) (=KACC 17155(T) = NCIMB 14829(T) = DSM 45801(T)).

Catheter-associated Nocardia higoensis bacteremia in a child with acute lymphocytic leukemia

A 23-month-old child with leukemia who was receiving chemotherapy developed fevers. Serial blood cultures from a central venous catheter and a peripheral venous site grew an organism identified by 16S rRNA gene sequencing and phenotypic analysis as Nocardia higoensis, an opportunistic organism isolated once previously from a pulmonary infection in Japan.

A Case of Cutaneous Nocardiosis with Involvement of the Trachea, Anterior Mediastinum and Sternum

Nocardiosis is a rare infectious disease due to Nocardia infections. In this report, we present a rare case of cutaneous nocardiosis with involvement of the trachea, anterior mediastinum and sternum. The strain of Nocardia has been isolated from bacterial culture of infected tissue. 16s rRNA sequencing confirmed that it contained the Nocardia genus. The patient was successfully treated with Co-SMZ.

secA1 gene sequence polymorphisms for species identification of Nocardia species and recognition of intraspecies genetic diversity

Sequence analysis of the Nocardia essential secretory protein SecA1 gene (secA1) for species identification of 120 American Type Culture Collection (ATCC) and clinical isolates of Nocardia (16 species) was studied in comparison with 5'-end 606-bp 16S rRNA gene sequencing. Species determination by both methods was concordant for all 10 ATCC strains. secA1 gene sequencing provided the same species identification as 16S rRNA gene analysis for 94/110 (85.5%) clinical isolates. However, 40 (42.6%) isolates had sequences with <99.0% similarity to archived secA1 sequences for the species, including 29 Nocardia cyriacigeorgica (96.6 to 98.9% similarity) and 4 Nocardia veterana (91.5 to 98.9% similarity) strains. Discrepant species identification was obtained for 16 (14.5%) clinical isolates, including 13/23 Nocardia nova strains (identified as various Nocardia species by secA1 sequencing) and 1 isolate each of Nocardia abscessus (identified as Nocardia asiatica), Nocardia elegans (Nocardia africana), and Nocardia transvalensis (Nocardia blacklockiae); both secA1 gene sequence analysis and deduced amino acid sequence analysis determined the species to be different from those assigned by 16S rRNA gene sequencing. The secA1 locus showed high sequence diversity (66 sequence or genetic types versus 40 16S rRNA gene sequence types), which was highest for N. nova (14 secA1 sequence types), followed by Nocardia farcinica and N. veterana (n = 7 each); there was only a single sequence type among eight Nocardia paucivorans strains. The secA1 locus has potential for species identification as an adjunct to 16S rRNA gene sequencing but requires additional deduced amino acid sequence analysis. It may be a suitable marker for phylogenetic/subtyping studies.

Evaluation of the integrated database network system (IDNS) SmartGene software for analysis of 16S rRNA gene sequences for identification of Nocardia species

16S rRNA gene sequences of 102 Nocardia isolates were analyzed using the Integrated Database Network System (IDNS) SmartGene centroid database. A total of 76% of the isolates were correctly identified. Discordant identifications were due to inadequate centroid length (3 species), inaccurate or insufficient entries in the public databases (5 species), and heterogeneous sequences among members of a species (1 species).

Nocardia wallacei sp. nov. and Nocardia blacklockiae sp. nov., human pathogens and members of the "Nocardia transvalensis Complex"

Nocardia isolates that share the property of in vitro amikacin resistance are grouped together by some authors in the Nocardia transvalensis complex. Our examination of 13 isolates that are amikacin resistant has revealed the existence of three distinct species. Sequence analysis of the 16S rRNA, 65-kDa heat shock protein, and secA1 genes, coupled with DNA-DNA hybridization, indicated that "N. asteroides drug pattern IV," "N. transvalensis new taxon 1," and N. transvalensis sensu stricto should each be considered a distinct species. The phenotypic and molecular characteristics of the proposed new species Nocardia wallacei (N. asteroides drug pattern IV) and N. blacklockiae (N. transvalensis new taxon 1) are presented and compared with those of N. transvalensis sensu stricto. The relative genetic diversity of isolates best placed with the species N. blacklockiae is also discussed. Case studies demonstrating the pathogenicity of N. wallacei and N. blacklockiae are presented. The type strain of N. wallacei is ATCC 49873 (DSM 45136), and that of N. blacklockiae is ATCC 700035 (DSM 45135).

Nocardia nova as the causative agent in spondylodiscitis and psoas abscess

We describe here the first case of Nocardia nova spondylodiscitis accompanied by a psoas abscess due to spreading from pulmonary nocardiosis. Nocardia was cultured from all affected sites. After 1 year of an appropriate antimicrobial therapy and a surgical drainage of the abscess that was required, the patient's clinical condition had improved.

Nocardia nova as the causative agent in spondylodiscitis and psoas abscess

We describe here the first case of Nocardia nova spondylodiscitis accompanied by a psoas abscess due to spreading from pulmonary nocardiosis. Nocardia was cultured from all affected sites. After 1 year of an appropriate antimicrobial therapy and a surgical drainage of the abscess that was required, the patient's clinical condition had improved.

Analysis of multiple differing copies of the 16S rRNA gene in five clinical isolates and three type strains of Nocardia species and implications for species assignment

Five clinical isolates of Nocardia that showed ambiguous bases within the variable region of the 16S rRNA gene sequence were evaluated for the presence of multiple copies of this gene. The type strains of three Nocardia species, Nocardia concava, Nocardia ignorata, and Nocardia yamanashiensis, which also showed ambiguous bases in the variable region, were also examined. Cloning experiments using an amplified region of the 16S rRNA that contains the variable region showed that each isolate possessed 16S rRNA genes with at least two different sequences. In addition, hybridization studies using a 16S rRNA gene-specific probe and extracted genomic DNA of the patient isolates and of the type strain of N. ignorata showed that each isolate possessed at least three copies of the gene. These multiple differing copies of the 16S rRNA gene and the results of DNA-DNA hybridization studies indicate problems of species definition and identification for such isolates. A broader species concept than that currently in vogue may be required to accommodate such organisms.

Analysis of secA1 gene sequences for identification of Nocardia species

Molecular methodologies, especially 16S rRNA gene sequence analysis, have allowed the recognition of many new species of Nocardia and to date have been the most precise methods for identifying isolates reliably to the species level. We describe here a novel method for identifying Nocardia isolates by using sequence analysis of a portion of the secA1 gene. A region of the secA1 gene of 30 type or reference strains of Nocardia species was amplified using secA1-specific primers. Sequence analysis of 468 bp allowed clear differentiation of all species, with a range of interspecies similarity of 85.0% to 98.7%. Corresponding 16S rRNA gene sequences of a 1,285-bp region for the same isolates showed a range of interspecies similarity of 94.4 to 99.8%. In addition to the type and reference strains, a 468-bp fragment of the secA1 gene was sequenced from 40 clinical isolates of 12 Nocardia species previously identified by 16S rRNA gene sequence analysis. The secA1 gene sequences of most isolates showed >99.0% similarity to the secA1 sequences of the type or reference strain to which their identification corresponded, with a range of 95.3 to 100%. Comparison of the deduced 156 amino acid sequences of the SecA1 proteins of the clinical isolates showed between zero and two amino acid residue differences compared to that of the corresponding type or reference strain. Sequencing of the secA1 gene, and using deduced amino acid sequences of the SecA1 protein, may provide a more discriminative and precise method for the identification of Nocardia isolates than 16S rRNA gene sequencing.

Determination of antimicrobial susceptibility patterns of Nocardia spp. from clinical specimens by Etest

Susceptibilities to 11 antimicrobial agents were determined by Etest for 93 Nocardia isolates from clinical specimens and 15 type strains belonging to different Nocardia spp. All isolates were susceptible to trimethoprim-sulphamethoxazole, amikacin and linezolid, but susceptibilities of the various Nocardia spp. to beta-lactams, aminoglycosides, ciprofloxacin and clarithromycin varied markedly. Overall, there was a good correlation between the drug resistance patterns and the species identification established by conventional phenotypic tests and 16S rDNA sequencing. Among the different species encountered, Nocardia farcinica and Nocardia brasiliensis displayed the most multiresistant profiles, with resistance to imipenem occurring mainly among isolates of N. brasiliensis and Nocardia abscessus. The species variability in susceptibility profiles and the numerous recent taxonomic changes means that in-vitro susceptibility tests may be a complementary tool for the identification of Nocardia isolates from human clinical specimens. Further studies on a larger number of species from more diverse geographical sources, including species that are found less commonly among clinical isolates, are required to validate and extend the results.

Capillary electrophoresis and the clinical laboratory

Over the past 15 years, CE as an analytical tool has shown great promise in replacing many conventional clinical laboratory methods, such as electrophoresis and HPLC. CE's appeal was that it was fast, used very small amounts of sample and reagents, was extremely versatile, and was able to separate large and small analytes, whether neutral or charged. Because of this versatility, numerous methods have been developed for analytes that are of clinical interest. Other than molecular diagnostic and forensic laboratories CE has not been able to make a major impact in the United States. In contrast, in Europe and Japan an increasing number of clinical laboratories are using CE. Now that automated multicapillary instruments are commercially available along with cost-effective test kits, CE may yet be accepted as an instrument that will be routinely used in the clinical laboratories. This review will focus on areas where CE has the potential to have the greatest impact on the clinical laboratory. These include analyses of proteins found in serum and urine, hemoglobin (A1c and variants), carbohydrate-deficient transferrin, forensic and therapeutic drug screening, and molecular diagnostics.

Nocardia gamkensis sp. nov

A novel actinomycete, strain CZH20(T), was isolated from a soil sample taken from the banks of the Gamka River in the Swartberg Nature Reserve, Western Cape Province, South Africa. Strain CZH20(T) was identified as a member of the genus Nocardia by a polyphasic approach. Strain CZH20(T) could be differentiated from other members of the genus Nocardia on the basis of physiology and 16S-rRNA gene sequence analysis. It exhibited weak antibiosis against Mycobacterium aurum A+. Organic solvent extracts of the culture filtrate and mycelial mass of CZH20(T) exhibited moderate antibiotic activity against Mycobacterium smegmatis LR222 and Mycobacterium tuberculosis H37Rv. The name Nocardia gamkensis is proposed, with the type strain CZH20(T) (=DSM 44956(T) =NRRL B-24450(T)).

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.

Nocardia exalbida sp. nov., isolated from Japanese patients with nocardiosis

Two bacterial strains isolated from different hospitals in Japan were subjected to a polyphasic analysis. Strains IFM 0803T and IFM 10383 were found to have morphological, biochemical, physiological and chemotaxonomic properties consistent with their classification in the genus Nocardia. Strains IFM 0803T and IFM 10383 clustered with the type strain of Nocardia xishanensis, showing 16S rRNA gene sequence similarities of 98.6–98.9 % with this species. The novel strains could be distinguished from N. xishanensis by a range of phenotypic properties. Based on their phenotypic and phylogenetic characteristics, the two isolates are proposed as members of a novel species of the genus Nocardia, Nocardia exalbida sp. nov., with the type strain IFM 0803T (=NBRC 100660T=JCM 12667T=DSM 44883T).

Distribution of nocardia species in clinical samples and their routine rapid identification in the laboratory

Eighty-six Nocardia strains isolated from clinical samples in Belgium were identified by 16S rRNA gene sequencing. Eighty-three (96%) strains belonged to only six Nocardia species: N. farcinica (38 [44%]), N. nova (19 [22%]), N. cyriacigeorgica (13 [15%]), N. brasiliensis (6 [6.9%]), N. abscessus (5 [5.8%]), and N. paucivorans (2 [2.3%]). A gallery of nine conventional and enzymatic tests was developed for the rapid identification of the most common species isolated during this survey. Pyrrolidonyl aminopeptidase, gamma-glutamyl aminopeptidase, alpha-mannosidase, and alpha-glucosidase were found to be highly discriminating and could be used to develop an identification scheme.

Validation of publication of new names and new combinations previously effectively published outside the IJSEM

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.