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

Resistance to rifampicin: at the crossroads between ecological, genomic and medical concerns

The first antibiotic of the ansamycin family, rifampicin (RIF), was isolated in 1959 and was introduced into therapy in 1962; it is still a first-line agent in the treatment of diseases such as tuberculosis, leprosy and various biofilm-related infections. The antimicrobial activity of RIF is due to its inhibition of bacterial RNA polymerase (RNAP). Most frequently, bacteria become resistant to RIF through mutation of the target; however, this mechanism is not unique. Other mechanisms of resistance have been reported, such as duplication of the target, action of RNAP-binding proteins, modification of RIF and modification of cell permeability. We suggest that several of these alternative resistance strategies could reflect the ecological function of RIF, such as autoregulation and/or signalling to surrounding microorganisms. Very often, resistance mechanisms found in the clinic have an environmental origin. One may ask whether the introduction of the RIF analogues rifaximin, rifalazil, rifapentine and rifabutin in the therapeutic arsenal, together with the diversification of the pathologies treated by these molecules, will diversify the resistance mechanisms of human pathogens against ansamycins.

Nocardia cyriacigeorgica: a case of endocarditis with disseminated soft-tissue infection

Nocardia cyriacigeorgica is a common environmental organism. It has been isolated from clinical samples in Europe, Asia and North America, predominantly from respiratory samples but also from samples from several other sites. We present a case report of an 85-year-old female patient in the UK who was found to have a multi-focal soft-tissue infection from which N. cyriacigeorgica was isolated. She had a background history of chronic obstructive pulmonary disease and corticosteroid use for polymyalgia rheumatica. During the course of her treatment echocardiography showed the presence of a mobile heart mass attached to a valve leaflet, a major Dukes criterion for endocarditis. We suggest that in cases of disseminated Nocardia infection, endocarditis should be tested for, particularly in cases failing to respond to treatment. We also review previous reports of both N. cyriacigeorgica infection, and of endocarditis due to Nocardia species and related genera.

Nocardia iowensis sp. nov., an organism rich in biocatalytically important enzymes and nitric oxide synthase

Nocardia strain NRRL 5646, isolated from a garden soil sample in Osceola, Iowa, USA, was initially of interest as an antibiotic producer. It contained biocatalytically important enzymes and represented the first described nitric oxide synthase enzyme system in bacteria. The present polyphasic taxonomic study was undertaken to differentiate strain NRRL 5646(T) from related species of the genus Nocardia. Chemotaxonomic analyses included determinations of the fatty acid methyl ester profile (C(16 : 1)omega6c/C(16 : 1)omega7c, C(16 : 0), C(18 : 1)omega9c and C(18 : 0) 10-methyl as major components), quinone [cyclo MK-8(H(4)) as the major component], polar lipid (diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside as major components) and mycolic acid. These results supported its placement within the genus Nocardia. Biochemical testing and 16S rRNA, 65-kDa heat-shock protein (hsp65) and preprotein translocase (secA1) gene sequence analyses differentiated strain NRRL 5646(T) from recognized Nocardia species. Previous studies have demonstrated that other genetic sequences (carboxylic acid reductase, Nocardia phosphopantetheinyl transferase and GTP cyclohydrolase I) from strain NRRL 5646(T) can also be used to substantiate its uniqueness. The level of 16S rRNA gene sequence similarity between strain NRRL 5646(T) and the type strains of Nocardia tenerifensis and Nocardia brasiliensis was 98.8 %. However, strain NRRL 5646(T) could be clearly distinguished from these Nocardia species based on DNA-DNA hybridization data. Consequently, strain NRRL 5646(T) is considered to represent a novel species of the genus Nocardia, for which the name Nocardia iowensis sp. nov. is proposed. The type strain is NRRL 5646(T) (=UI 122540(T)=NRRL B-24671(T)=DSM 45197(T)).

Assignment of reference 5'-end 16S rDNA sequences and species-specific sequence polymorphisms improves species identification of Nocardia

16S rDNA sequence analysis is the most accurate method for definitive species identification of nocardiae. However, conflicting results can be found due to sequence errors in gene databases. This study tested the feasibility of species identification of Nocardia by partial (5’-end 606-bp) 16S rDNA sequencing, based on sequence comparison with “reference” sequences of well-annotated strains. This new approach was evaluated using 96 American Type Culture Collection (n=6), and clinical (n=90) Nocardia isolates. Nucleotide sequence-based polymorphisms within species were indicative of “sequence types” for that species. Sequences were compared with those in the GenBank, Bioinformatics Bacteria Identification and Ribosomal Database Project databases. Compared with the reference sequence set, all 96 isolates were correctly identified using the criterion of ≥99% sequence similarity. Seventy-eight (81.3%) were speciated by database comparison; alignment with reference sequences resolved the identity of 14 (15%) isolates whose sequences yielded 100% similarity to sequences in GenBank under >1 species designation. Of 90 clinical isolates, the commonest species was Nocardia nova (33.3%) followed by Nocardia cyriacigeorgica (26.7%). Recently-described or uncommon species included Nocardia veterana (4.4%), Nocarida bejingensis (2.2%) and, Nocardia abscessus and Nocardia arthriditis (each n=1). Nocardia asteroides sensu stricto was rare (n=1). There were nine sequence types of N. nova, three of Nocardia brasiliensis with two each of N. cyriacigeorgica and Nocardia farcinica. Thirteen novel sequences were identified. Alignment of sequences with reference sequences facilitated species identification of Nocardia and allowed delineation of sequence types within species, suggesting that such a barcoding approach can be clinically useful for identification of bacteria.

Disseminated systemic Nocardia farcinica infection complicating alefacept and infliximab therapy in a patient with severe psoriasis

Nocardiosis is a cause of significant morbidity and mortality in the immunocompromised host, and is an infrequent complication of tumor necrosis factor alpha (TNF-alpha) blockers in chronic inflammatory diseases. Nocardiosis occurs at a rate of 3.55 and 0.88 per 100 000 patients treated with infliximab or etanercept, respectively. Disseminated nocardiosis remains an uncommon complication of these agents. Here, we present a fatal case of disseminated systemic nocardiosis in a patient with psoriasis following sequential therapy with alefacept and then infliximab therapy. The patient developed disseminated disease involving the brain, lymph nodes, and adrenal glands. The diagnosis was made by blood culture and aspiration of the adrenal gland abscess, which revealed Gram-positive bacilli and later grew Nocardia farcinica. The organism was identified by DNA sequencing, and was susceptible to moxifloxacin, gatifloxacin, ciprofloxacin, amoxicillin-clavulanic acid, linezolid, sulfamethoxazole, and amikacin. It was resistant to clarithromycin, ceftriaxone, and tobramycin and was intermediately susceptible to imipenem.

Pulmonary nocardiosis: risk factors, clinical features, diagnosis and prognosis

PURPOSE OF REVIEW

Pulmonary infection by Nocardia spp. has been recognized for the past 100 years. The number of cases of pulmonary nocardiosis reported in the literature is increasing, and in some cases, a diagnosis is reached even postmortem. This increase is partly due to the growing number of patients with depressed cellular immunity. The diagnosis of this infection, which has a high rate of mortality, is usually delayed, due to a nonspecific clinical-radiological presentation and the difficulties in cultivating the bacteria. This review analyzes the current situation, in order to better understand this infection and enhance awareness and clinical suspicion that would lead to further specific microbiological studies and treatment.

RECENT FINDINGS

The number of case series in the literature is increasing. This development may be due to an absolute increase in the number of immunocompromised patients, but also to improvements in laboratory techniques and molecular methods to detect nocardiosis.

SUMMARY

It is important to keep in mind, and suspect the presence of pulmonary nocardiosis in the immunodepressed patients with clinical pulmonary infection. Furthermore, the laboratory should be notified when Nocardia is suspected in a clinical specimen so that measures can be taken to optimize recognition and recovery of the organism.

Disseminated subcutaneous nocardiosis caused by Nocardia farcinica diagnosed by FNA biopsy and 16S ribosomal gene sequencing

Nocardia is an infrequent but significant cause of infections in the immunocompromised host. Clinical syndromes are varied and ranges from pulmonary, disseminated, cutaneous, and CNS involvement. Here we describe a case of disseminated subcutaneous nodules in a patient with multiple myeloma caused by Nocardia farcinica. The diagnosis was made by FNA biopsy which revealed gram positive filamentous bacilli in background of acute inflammation on smears. This was confirmed by 16S ribosomal gene sequencing. Prompt identification of N. farcinica is important because of its intrinsic resistance to broad spectrum cephalosporins and high risk of dissemination.

Nocardia cyriacigeorgica, an emerging pathogen in the United States

Nocardia cyriacigeorgica is recognized as an emerging pathogen in many parts of the world. We present the first case description of invasive N. cyriacigeorgica pulmonary infection in the United States identified to the species level by 16S rRNA and hsp65 sequence analysis. A subsequent retrospective molecular screening of recent Nocardia clinical isolates at our New York City medical center yielded an additional six N. cyriacigeorgica isolates. Because routine laboratory algorithms for the phenotypic identification of Nocardia species are limited in practice, the true prevalence of N. cyriacigeorgica infections may be greater than currently appreciated. Indeed, we present evidence confirming that N. cyriacigeorgica is coincident with the unofficial species designation Nocardia asteroides complex antimicrobial susceptibility pattern type VI and distinct from the N. asteroides sensu stricto strain ATCC 19247(T). As nocardial species identity can predict antimicrobial susceptibility and guide clinical management, we offer simplified phenotypic and molecular protocols to assist the identification of N. cyriacigeorgica.

Isolation of Nocardia asiatica from cutaneous ulcers of a human immunodeficiency virus-infected patient in Italy

A strain of Nocardia was isolated from cutaneous ulcers of a human immunodeficiency virus-infected patient in Italy. Comparative 16S rRNA gene sequence analysis revealed that the isolate represented a strain of Nocardia asiatica. Antimicrobial susceptibility testing was essential to guide the clinicians to successfully treat this infection.

Clinical and microbiological features of nocardiosis 1997–2003

Nocardiosis has been believed to be caused by the members of the Nocardia asteroides complex and the Nocardia brasiliensis species. However, recent advances in genotypic identification have shown that the genus exhibits considerable taxonomic complexity and the phenotypic markers used in the past for its identification can be ambiguous. The aim of this study was to assess the species distribution of Nocardia isolates and to determine whether there are differences in pathogenicity or antimicrobial susceptibility between the different species identified. Nocardia isolates obtained over a 7 year period were retrospectively reviewed. The isolates were identified genotypically, their antibiotic susceptibility was tested and the clinical data of the 27 patients were retrieved. Eight different Nocardia species were identified: Nocardia farcinica (n=9), Nocardia abscessus (n=6), Nocardia cyriacigeorgica (n=6), Nocardia otitidiscaviarum (n=2), Nocardia nova (n=1), N. nova complex (n=1), Nocardia carnea (n=1) and Nocardia transvalensis complex (n=1). All species were susceptible to co-trimoxazole but different patterns of susceptibility to other agents were observed. All patients had active comorbidities at the time of infection. A total of 19 patients were immunosuppressed, due to human immunodeficiency virus infection, chronic corticosteroid therapy, immunosupressive therapy or haematological malignancies. Six patients displayed a Charlson comorbidity index score above 4. Global mortality was 50 % while attributable mortality was 34.6 %. Patients infected with N. farcinica – the most resistant species – had the highest Charlson index score and the highest mortality rate. Accurate identification of the species and susceptibility testing of Nocardia isolates may play an important role in diagnosis and treatment.

Thiols in nitric oxide synthase-containing Nocardia sp. strain NRRL 5646

Mycothiol (MSH) [1-D-myo-inosityl-2-(N-acetyl-l-cysteinyl)amido-2-deoxy-alpha-D-glucopyranoside], isolated as the bimane derivative, was established to be the major thiol in Nocardia sp. strain NRRL 5646, a species most closely related to Nocardia brasiliensis strain DSM 43758(T). Thiol formation and detection of MSH-dependent formaldehyde dehydrogenase activity in cell extracts are relevant to the possible modulation of nitric oxide toxicity generated by strain NRRL 5646.

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.

Nocardia paucivorans – A cause of disseminated Nocardiosis

We describe a 53-year-old man without discernable immunocompromise who presented with cerebral and cutaneous dissemination of primary pulmonary Nocardia paucivorans infection. This report also identifies 32 other patients in our health area with clinical isolates of N. paucivorans over the last 20 years, extending the reported spectrum of disease caused by this organism. At least 30% (10/33) of these patients had disseminated disease indicating a propensity of this species to disseminate.

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.

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.

Contribution of rpoB2 RNA polymerase beta subunit gene to rifampin resistance in Nocardia species

Nocardia species are gram-positive environmental saprophytes, but some cause the infectious disease nocardiosis. The complete genomic sequence of Nocardia farcinica IFM 10152 has been determined, and analyses indicated the presence of two different RNA polymerase beta subunit genes, rpoB and rpoB2, in the genome (J. Ishikawa, A. Yamashita, Y. Mikami, Y. Hoshino, H. Kurita, K. Hotta, T. Shiba, and M. Hattori, Proc. Natl. Acad. Sci. USA 101:14925-14930, 2004). These genes share 88.8% identity at the nucleotide level. Moreover, comparison of their amino acid sequences with those of other bacterial RpoB proteins suggested that the nocardial RpoB protein is likely to be rifampin (RIF) sensitive, whereas RpoB2 protein contains substitutions at the RIF-binding region that are likely to confer RIF resistance. Southern analysis indicated that rpoB duplication is widespread in Nocardia species and is correlated with the RIF-resistant phenotype. The introduction of rpoB2 by using a newly developed Nocardia-Escherichia coli shuttle plasmid vector and transformation system conferred RIF resistance to Nocardia asteroides IFM 0319T, which has neither RIF resistance nor rpoB duplication. Furthermore, unmarked rpoB2 deletion mutants of N. farcinica IFM 10152 showed no significant resistance to RIF. These results indicated the contribution of rpoB2 to RIF resistance in Nocardia species. Since this is the first example of genetic engineering of the Nocardia genome, we believe that this study, as well as our determination of the N. farcinica genome sequence, will be a landmark in Nocardia genetics.

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.

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.