Outbreak of Nocardia farcinica infection with the same pattern in randomly amplified polymorphic DNA analysis

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.

Disseminated nocardiosis caused by Nocardia farcinica in a patient with colon cancer: A case report and literature review

RATIONALE

Nocardiosis is an uncommon and potentially life-threatening infection that usually affects immunocompromised hosts. No clinical guidelines have been established for managing this rare disease, and the optimal treatment modality remains unclear. Nocardia farcinica, a relatively infrequent pathogen of nocardiosis, causes a clinically aggressive infection. In addition to our patient data, our search of the literature for patients who presented with empyema caused by N. farcinica will provide fundamental information for optimal treatment modalities.

PATIENT CONCERNS

A 64-year-old man was diagnosed with empyema, 4 days following surgery for sigmoid colon cancer. Brain lesions were evaluated only after N. farcinica was isolated and identified as the causative pathogen through repeated culture tests.

DIAGNOSES

N. farcinica was isolated from the pleural effusion and confirmed as the pathogen through 16S rRNA sequencing.

INTERVENTIONS

The patient was successfully treated with tube thoracotomy, neurosurgical evacuation, and a combination of trimethoprim/sulfamethoxazole plus imipenem. Long-term antibiotic therapy was required to prevent recurrence.

OUTCOMES

Pyothorax showed a good clinical response to antimicrobial therapy and drainage of pleural effusion, whereas brain abscess did not respond to medical therapy and required surgery. The patient eventually recovered and continued chemotherapy as treatment for sigmoid colon cancer.

LESSONS

Although extremely rare, this report demonstrates the importance of considering Nocardia infection as the differential diagnosis in immunocompromised patients who present with empyema. In particular, because of the N. farcinica infection's tendency to spread and the resistance of the organism to antibiotics, aggressive evaluation of metastatic lesions and standardized support from microbiological laboratories are important. Surgery may be required in some patients with brain abscesses to improve the chance of survival.

Isolated Nocardiosis, an Unrecognized Primary Immunodeficiency?

Nocardiosis is an infectious disease caused by the gram-positive bacterium Nocardia spp. Although it is commonly accepted that exposure to Nocardia is almost universal, only a small fraction of exposed individuals develop the disease, while the vast majority remain healthy. Nocardiosis has been described as an "opportunistic" disease of immunocompromised patients, suggesting that exposure to the pathogen is necessary, but a host predisposition is also required. Interestingly, increasing numbers of nocardiosis cases in individuals without any detected risk factors, i.e., without overt immunodeficiency, are being reported. Furthermore, a growing body of evidence have shown that selective susceptibility to a specific pathogen can be caused by a primary immunodeficiency (PID). This raises the question of whether an undiagnosed PID may cause nocardiosis affecting otherwise healthy individuals. This review summarizes the specific clinical and microbiological characteristics of patients with isolated nocardiosis published during the past 30 years. Furthermore, it gives an overview of the known human immune mechanisms to fend off Nocardia spp. obtained from the study of PIDs and patients under immunomodulatory therapies.

Nocardiosis: A Neglected Disease

Nocardiosis is a neglected tropical disease. It has varied geographical presence and a spectrum of clinical presentations. This review aims to focus on the epidemiology of nocardial infections with a systematic approach to their diagnosis and treatment. Nocardiacauses chronic infections and ailments, and may remain cryptic but progressive in its course. Unless suspected, diagnosis can be easily missed resulting in increased morbidity and mortality. Thorough knowledge of local epidemiology, demography, clinical course and presentation, diagnostic modalities, and antibiotic susceptibility patterns of the prevalent Nocardia species is essential to curb spread of this infection. This is a systematic review in which internet search has been done for citation indices (Embase, PubMed, Ovid, and other individual journals) till March 2020 utilizing the following key words "Nocardia," "taxonomy," "prevalence," "clinical features," "diagnosis," "treatment," and "susceptibility." We selected a total of 87 review articles, case series, and case reports all in English language.

Altered thymic CD4+ T-cell recovery after allogeneic hematopoietic stem cell transplantation is critical for nocardiosis

PURPOSE OF THE STUDY

Nocardia affects immunocompromised human host exhibiting an altered cell-mediated immunity. Infectious risk after allogeneic hematopoietic cell transplantation (AHCT) is significantly correlated to the recovery status of donor-derived immune system, especially CD4⁺ T-cells reconstitution and thymopoiesis. The purpose of this paper is to highlight a lack of cell-mediated immunity recovery for patients presenting a nocardiosis compared to a control cohort.

PATIENTS AND METHODS

This is a case control retrospective monocentric study. We retrospectively analyzed a monocentric cohort of 15 cases of nocardiosis after AHCT and we explored the degree of patients' immunosuppression by phenotyping circulating lymphoid subpopulations, including NK cells, CD8⁺ T-cells, CD4⁺ T-cells and CD19⁺ B-cells. We focused on CD4⁺ T-cell subsets to appreciate thymic output, especially on naive CD4⁺ T-cells (NTE, CD45RA⁺/RO^- CD4⁺ T-cells) and recent thymic emigrants (RTE, CD4⁺CD45RA⁺/RO^-/CD31⁺). Infected patients were paired with a control cohort of patients with identical transplantation characteristics screened on hematological disease, AHCT conditioning, primary graft-versus-host disease (GHVD) prophylaxis, graft type, sex, age, and season at the AHCT and data concerning immunological reconstitution were compared.

RESULTS

At onset of nocardiosis, circulating lymphocytes and CD4⁺ T-cells means count were respectively 730/μL and 162/μL. CD8⁺ T-cells, CD56⁺ NK cells and CD19⁺ B-cells means count were respectively 362/μL, 160/μL, 112/μL. CD4⁺ T-cells subpopulations, naïve CD4⁺ T-cells production was impaired with NTE and RTE means count at 26/μL and 11/μL respectively. Comparison between nocardiosis cohort and control cohort over time highlight significant lower cellular count for lymphocytes, CD4⁺ T-cells, NTE and RTE with p = 0.001, p < 0.001, p < 0.001, p < 0.001 respectively.

CONCLUSION

Immune recovery monitoring follow-up after AHCT is of particular importance to identify patients susceptible to develop Nocardiosis. Efficient microbiological investigations toward Nocardia such PCR should be used in case of compatible clinical presentation.

Molecular analysis and species diversity of Nocardia in the hospital environment in a developing country, a potential health hazard

PURPOSE

Despite hundreds of reports on the isolation of Nocardia from clinical samples, the presence and diversity of Nocardia species that are capable of survival in a harsh and adverse condition, such as a hospital environment, have not been comprehensively studied. The aim of this study was to assess Nocardia species diversity in a hospital environment to provide a better insight into their potential threat as a reservoir for the development of nosocomial infections.

METHODOLOGY

A total of 90 samples of hospital water, dust and soil, collected from 30 hospitals, were analysed for the presence of Nocardia using standard protocols for isolation and characterization of the isolates. Conventional tests were used for preliminary identification, and PCR amplification of the 596 bp amplicon of the 16S rRNA and sequence analysis of 16S rRNA were performed for genus and species identification.

RESULTS

A total of 25 Nocardia isolates (27.7 %) from 10 species were recovered from 90 samples. The three most prevalent species were N. cyriacigeorgica, 24 %, N. asteroides, 16 % and N. kroppenstedtii, 12 %, followed by N. salmonicida-like, 8 % and single isolates of N.otitidiscaviarum, N. flavorozea-like, N. neocaledoniensis-like and N. sungurluensis-like. Thirteen out of twenty five isolates showed characteristics of six novel species.

CONCLUSION

Our study showed that the hospital environment is a potential reservoir of a diverse range of Nocardia species, due to the remarkable survival capability of these bacteria in an adverse hospital environment, which carries a threat to the health of patients.

Disseminated Nocardia farcinica: literature review and fatal outcome in an immunocompetent patient

BACKGROUND

Nocardia farcinica is a gram-positive, partially acid-fast, methenamine silver-positive aerobic actinomycete. Nocardia spp. are opportunistic pathogens, and N. farcinica is the least common species of clinical importance.

METHODS

Review of the recent literature and description of a immunocompetent patient with no known risk factors who contracted fatal N. farcinica sepsis.

RESULTS

Positive pre-mortem and post-mortem cultures from the lung and synovium correlated with acute bronchopneumonia and synovitis at autopsy. Colonies of filamentous bacteria, which were not apparent in conventional hematoxylin and eosin-stained sections, were observed with gram and methenamine silver stains, but acid-fast stains were negative. A literature review revealed that disseminated N. farcinica often is associated with an underlying malignant tumor or autoimmune disease (88% of patients). Chemotherapy or corticosteroid treatments are additional risk factors.

CONCLUSIONS

Trimethoprim-sulfamethoxazole typically is the first-line therapy for N. farcinica; treatment with amikacin and imipenem-cilastatin is used less often (7% of patients). Despite aggressive therapy, we observed that the death rate (39%) associated with N. farcinica in recent publications was eight percentage points higher than reported in a review from 2000.

Phylogenetic analysis of rRNA methyltransferases, Erm and KsgA, as related to antibiotic resistance

It has long been speculated that erm and ksgA are related evolutionarily due to their sequence similarity and analogous catalytic reactions. We performed a comprehensive phylogenetic analysis with extensive Erm and KsgA/Dim1 sequences (Dim1 is the eukaryotic ortholog of KsgA). The tree provides insights into the evolutionary history of erm genes, showing early bifurcation of the Firmicutes and the Actinobacteria, and suggesting that the origin of the current erm genes in pathogenic bacteria cannot be explained by recent horizontal gene transfer from antibiotic producers. On the other hand, the phylogenetic analysis cannot support the commonly assumed phylogenetic relationships between erm and ksgA genes, the common ancestry of erm and ksgA or erm descended from preexisting ksgA, because the tree cannot be unequivocally rooted due to insufficient signal and long-branch attraction. The phylogenetic tree indicates that the erm gene underwent frequent horizontal gene transfer and duplication, resulting in phylogenetic anomalies and atypical phenotypes. Several electronically annotated Erm sequences were recognized as candidates for new classes of macrolide-lincosamide-streptogramin B-resistance determinants, sharing less than an 80% amino acid sequence identity with other Erm classes.

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.

Molecular typing of a suspected cluster of Nocardia farcinica infections by use of randomly amplified polymorphic DNA, pulsed-field gel electrophoresis, and amplified fragment length polymorphism analyses

Randomly amplified polymorphic DNA (RAPD), pulsed-field gelelectrophoresis (PFGE), and amplified fragment length polymorphism (AFLP) analyses were used to investigate a possible outbreak of Nocardia farcinica. RAPD and PFGE analyses yielded irreproducible and unsatisfactory results, respectively. AFLP analysis seem to be a promising and welcome addition for molecular analysis of Nocardia isolates.