Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 26, Number 3—March 2020
Research Letter

Pulmonary Nocardia ignorata Infection in Gardener, Iran, 2017

Article Metrics
citations of this article
EID Journal Metrics on Scopus
Hossein A. Rahdar, Mehrnaz A. Gharabaghi, Abbas Bahador, Shahram Shahraki-Zahedani, Morteza Karami-Zarandi, Shahram Mahmoudi, and Mohammad M. FeizabadiComments to Author 
Author affiliations: Iranshahr University of Medical Sciences, Iranshahr, Iran (H.A. Rahdar); Tehran University of Medical Sciences, Tehran, Iran (M.A. Gharabaghi, A. Bahador, M. Karami-Zarandi, S. Mahmoudi, M.M. Feizabadi); Zahedan University of Medical Sciences, Zahedan, Iran (S. Shahraki-Zahedani)

Cite This Article


Nocardia ignorata, which was first described in 2001, is a rare human pathogen. We report a case of pulmonary nocardiosis caused by this bacterium in a 55-year-old man from Iran. The patient, a gardener, had frequent exposure to soil and may have acquired the infection from that source.

Since the description of Nocardia ignorata in 2001 (1), 4 respiratory isolates in Europe and 3 corneal isolates in India have been reported (2,3). Among the respiratory isolates, only 2 were confirmed as the cause of disease (2). We report a case of pulmonary nocardiosis that was caused by Nocardia ignorata in a person from Iran.

The patient, a 55-year-old man, smoked, had multiple myeloma, and had a history of opium use for 3 years. He was consuming methadone syrup daily at the time of hospitalization but had no history of corticosteroid consumption. He had frequent exposure to dust because of working in a garden.

The recent course of disease began ≈4 months earlier, initially as a feeling of heaviness and pain in the anterior chest (no clear distribution) and shortness of breath (functional class II level). However, coronary disease was rejected as a possible diagnosis during examination. The patient had night sweats and a weight loss of 5% in the past 4 months.

Two months after initial symptoms began, he had had fever, chills, and gradually productive coughs. During a visit to a different hospital, he was given a diagnosis of bacterial pneumonia and received azithromycin and cefixime, which initially reduced the symptoms but did not completely resolve them. When he sought care at Imam Khomeini Hospital (Tehran, Iran) because he had symptoms including cramping abdominal pain, fever, and shortness of breath 4–7 days before the visit, he was first admitted to the emergency department and then transferred to the lung unit.

Vital signs of the patient at the time of hospitalization were temperature 37.6°C, blood pressure 135/75 mm Hg, heart rate 80 beats/min, respiratory rate 18 breaths/min, and O2 saturation 90%. Laboratory findings were increased leukocyte count (12,210 cells/mm3 with 68.8% neutrophils) and C-reactive protein level 65 mg/L (reference value <5 mg/L); thyroid function test results were within reference ranges. Examination of abdominal organs did not show organomegaly or any other indications of disease; prostate size and consistency were unremarkable by testicular and digital rectal examinations. Heart sounds were unremarkable, and cervical, axillary, and extracorporeal lymph nodes were also unremarkable. Examination of the lungs showed fine end inspiratory crackles in both lungs.

Chest radiograph showed a mediastinal mass from the periphery of the right main bronchus to the medial and lower branches and an extension to the posterior part (vertebral trunk and adjacent to the esophagus). The maximum size of the mass was 31 × 74 mm, and an air bronchogram showed opacities near the mass, suggesting postobstructive pneumonia.

The patient was given empirical pneumonia treatment with levofloxacin (750 mg/d) and ceftriaxone (1 g, 2×/d) for 8 days. For the mediastinal mass, the patient underwent endoscopic ultrasonography and bronchoscopy, but his symptoms did not resolve. In a spiral computed tomography scan of the thorax, we found patchy ground glass and nodular opacities that were spread in both lungs, especially in posterior and lateral segments of the left lower lobe, the posterior segment of the right lower lobe, lingular, and the right upper lobe. Thus, nocardiosis and tuberculosis examinations were recommended.

We performed a tuberculin skin test, and the intraderm response to tuberculin was absent. Moreover, mucosal erythema with inflammation were seen on a right lung bronchoscopic examination. We found abundant mucoid secretions, no endobronchial ulcers, and a white discharge without endobronchial ulcer in the left lung.

We then subjected a bronchoalveolar lavage specimen for microbiological cultures. No Mycobacterium growth was seen, but colonies suspected of being Nocardia species appeared on blood agar plates after 4 days of incubation. A modified Kinyoun acid-fast stain confirmed the partial acid-fast staining feature of the colonies.

We performed DNA extraction by using the modified Pitcher method (46) and a Nocardia-specific PCR with primers NG1 (5′-ACCGACCACAAGGGGG-3′) and NG2 (5′-GGTTGTAAACCTCTTTCGA-3′). We obtained positive results with this PCR and a resistance-to-lysozyme test, and confirmed the presence of Nocardia species. For accurate identification, we PCR amplified 16S rRNA and partial DNA gyrase B (gyrB) genes (4) and subjected PCR products to direct sequencing (GenBank accession nos. KY817987.1 for 16S rRNA and MN159177 for gyrB).

We performed a BLAST analysis ( by using the megablast algorithm. This analysis confirmed the identity as N. ignorata (16S rRNA coverage 100% and 99% identity with GenBank accession no. KM113026.1; gyrB coverage 100% and 100% identity with GenBank accession no. GQ496109.1).

Antimicrobial drug susceptibility testing (broth microdilution method) showed that the isolate was susceptible to trimethoprim/sulfamethoxazole, imipenem, amikacin, doxycycline, and linezolid and resistant to erythromycin, ceftriaxone, and ciprofloxacin. At this point, we gave the patient cotrimoxazole and imipenem for 20 days and then trimethoprim/sulfamethoxazole for 6 months. The clinical, biological, and radiologic outcomes of the treatment were optimal, and no recurrence occurred after 8 months.

N. ignorata is a rare human pathogen. However, soil samples have been described as a possible reservoir (2,7,8). Accordingly, this patient, who had frequent exposure to soil through his work as a gardener, might have acquired the infection from that source.

Dr. Rahdar is an assistant professor in the Department of Microbiology, School of Medicine, Iranshahr University of Medical Sciences, Iranshahr, Iran. His research interests are rare bacterial pathogens and antimicrobial resistance.



  1. Yassin  AF, Rainey  FA, Steiner  U. Nocardia ignorata sp. nov. Int J Syst Evol Microbiol. 2001;51:212731. DOIPubMedGoogle Scholar
  2. Rodríguez-Nava  V, Couble  A, Khan  ZU, Pérouse de Montclos  M, Brasme  L, Villuendas  C, et al. Nocardia ignorata, a new agent of human nocardiosis isolated from respiratory specimens in Europe and soil samples from Kuwait. J Clin Microbiol. 2005;43:616770. DOIPubMedGoogle Scholar
  3. Lalitha  P, Srinivasan  M, Rajaraman  R, Ravindran  M, Mascarenhas  J, Priya  JL, et al. Nocardia keratitis: clinical course and effect of corticosteroids. Am J Ophthalmol. 2012;154:934939.e1. DOIPubMedGoogle Scholar
  4. Pitcher  D, Saunders  N, Owen  R. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol. 1989;8:1516. DOIGoogle Scholar
  5. Rahdar  HA, Azadi  D, Shojaei  H, Daei-Naser  A. Molecular analysis and species diversity of Nocardia in the hospital environment in a developing country, a potential health hazard. J Med Microbiol. 2017;66:33441. DOIPubMedGoogle Scholar
  6. Laurent  FJ, Provost  F, Boiron  P. Rapid identification of clinically relevant Nocardia species to genus level by 16S rRNA gene PCR. J Clin Microbiol. 1999;37:99102. DOIPubMedGoogle Scholar
  7. Habibnia  S, Nasab  MR, Heidarieh  P, Bafghi  MF, Pourmand  MR, Eshraghi  SS. Phenotypic characterization of Nocardia spp. isolated from Iran soil microflora. International Journal of Environmental Health Enginering. 2015;4:20. DOIGoogle Scholar
  8. Salimi  F, Hamedi  J, Motevaseli  E, Mohammadipanah  F. Isolation and screening of rare Actinobacteria, a new insight for finding natural products with antivascular calcification activity. J Appl Microbiol. 2018;124:25466. DOIPubMedGoogle Scholar


Cite This Article

DOI: 10.3201/eid2603.180725

Original Publication Date: February 04, 2020

Table of Contents – Volume 26, Number 3—March 2020

EID Search Options
presentation_01 Advanced Article Search – Search articles by author and/or keyword.
presentation_01 Articles by Country Search – Search articles by the topic country.
presentation_01 Article Type Search – Search articles by article type and issue.



Please use the form below to submit correspondence to the authors or contact them at the following address:

Mohammad M. Feizabadi, Department of Medical Microbiology, School of Medicine, Tehran University of Medical Sciences, Keshavarz Blvd, Poursina St, Tehran 1416753955, Iran

Send To

10000 character(s) remaining.


Page created: February 19, 2020
Page updated: February 19, 2020
Page reviewed: February 19, 2020
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.