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Int J Env Health Eng 2016,  5:24

First report of Gordonia terrae from Iran soil

1 Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
2 Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran

Date of Web Publication26-Dec-2016

Correspondence Address:
Mehdi Fatahi-Bafghi
Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/2277-9183.196667

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Gordonia terrae is the aerobic actinomycete that is microflora in soil. This study is the first report of Gordonia species from Iran soil and accurate identification in level species was obtained with conventional tests and 16S rRNA gene sequencing.

Keywords: 16S rRNA gene, Gordonia terrae, Iran, soil

How to cite this article:
Fatahi-Bafghi M, Andalibi F, Eshraghi SS. First report of Gordonia terrae from Iran soil. Int J Env Health Eng 2016;5:24

How to cite this URL:
Fatahi-Bafghi M, Andalibi F, Eshraghi SS. First report of Gordonia terrae from Iran soil. Int J Env Health Eng [serial online] 2016 [cited 2023 May 31];5:24. Available from:

  Introduction Top

Gordonia spp. are a Gram-positive coryneform bacterium [1] that isolated of various environmental sources.[2]Gordonia was first described in 1971 by Tsukamura of soil, and this bacterium was in the genus Rhodococcus previously.[1],[3]Gordonia terrae is one of the major pathogens in the genus Gordonia[4] and is cause various infections in human such as brain abscess,[5],[6] skin infection with lymphadenitis,[7] granulomatous mastitis,[8] and metatarsal osteomyelitis.[9] In the current paper, we describe the first report of G. terrae that isolated from Iran soil and accurate identification was done with phenotypic methods and 16S rRNA gene sequencing.

  Materials and Methods Top

Isolation method

The soil samples were collected for a survey of Nocardia species diversity from Iran soil.[10],[11],[12] This strain was isolated by paraffin baiting method (this method is not specific for Gordonia isolation and was isolated in our study accidentally) from one soil samples from North Khorasan, Iran.

Microbiological analysis

Our isolate has orange colonies on glass rod containing paraffin. Pure colonial of this bacterium was sub-cultured on nutrient agar and sabouraud dextrose agar containing the cycloheximide.

Phenotypic tests

This bacterium has orange pigmented colonies [Figure 1] and was pleomorphic rods in Gram-positive and partially acid-fast and was negative for kinyoun acid-fast staining. Results of phenotypic tests was: not growth in lysozyme broth and at 45°C, negative for aerial hyphae, negative for hydrolysis of urea, gelatin, esculin, tyrosine, hypoxanthine, xanthine, casein, positive for nitrate reductase, utilization of citrate, Acid production from sugars was positive for rhamnose and sucrose and was negative for sorbitol, glucose, L-arabinose, D-xylose, galactose, mannitol, lactose, and maltose, raffinose. Our isolate was suspicious to Gordonia spp., Rhodococcus spp., Tsukamurella spp. and Corynebacterium spp.
Figure 1: Orange colonial on nutrient agar medium

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DNA extraction

DNA genomic extraction was done the method described by Bafghi et al. previously.[13]

Full-length 16S rRNA gene sequencing

After DNA extraction from a pure culture of isolate for molecular accurate identification in the species level, sequencing, and analysis of 16S rRNA gene was done. Universal primers used in this study include: 27f (AGAGTTTGATCMTGGCTCAG) and 1525r (AAGGAGGTGWTCCARCC).[14] Sequence was analyzed with jPhydit software and using BLAST search of the National Institutes of Health GenBank database. The accession number for the 16S rRNA gene sequence of our strain is KP234025.

  Discussion Top

The first time, Tsukamura described the genus Gordona in 1971.[1] In 1977 and 1997, respectively, Goodfellow and Alderson reclassified members of the genus Gordona into the genus Rhodococcus due to the similarity of phenotypic and morphologic characterization [15] and this genus was renamed as Gordonia by Stackebrandt et al.[16]Gordonia species are extensively distributed in the environment, especially in soil. Members of this genus are aerobic, catalase-positive, partially acid-fast, non-motile, and Gram-positive rods.[1] Recently, 38 species of Gordonia has been identified by phenotypic and molecular techniques ( The genus Gordonia is an opportunistic pathogen in healthy individuals and particularly in patients with disorders of the immune system.[17],[18]Gordonia spp. can be misidentified when examined using phenotypic tests alone [19],[20] therefore, used the molecular methods such as 16S rRNA gene sequencing, HSP-RFLP, and gyrB gene sequencing.[21],[22],[23],[24] Full-sequence 16S rRNA gene sequencing is suitable for accurate identification in the genus Gordonia. Drancourt et al. reported G. terrae of brain abscess and central nervous system in 1994 and 1997, respectively.[5],[6] Gil-Sande et al. reported G. terrae ofacute cholecystitis in 2006.[20] Grisold et al. in 2007 reported G. terrae from a patient with catheter-related bacteremia.[25] Blanc et al. isolated G. terrae of palpebral abscess in 2007.[19] Lai et al. reported fifteen cases of Gordonia spp. such as Gordonia sputi and G. terrae from Taiwan, in 2010.[21] All articles listed were used of 16S rRNA gene sequencing for molecular identification. G. terrae is one of this species that have been misidentified as Rhodococcus because both genera have similar biochemical characteristics and most species have red to orange-pigmented colonies and commercial kits have not introduced for different them from the similar genus (aerobic actinomycetes).[1],[19],[21],[26] Gordonia, Nocardia and Tsukamurella are Gram-positive and partially acid-fast with non-Mycobacterium tuberculosis. The genus Nocardia growth in lysozyme broth and has aerial hyphae but Gordonia (Gordonia amarae and Gordonia defluvii exhibit aerial hyphae with microscopically), Tsukamurella and non-M. tuberculosis are negative for growth in lysozyme broth and aerial hyphae. Beta-galactosidase is positive in Tsukamurella and Nocardia.[20],[27],[28],[29],[30],[31],[32],[33] In conclusion, we have two recommendation for microbiologists that interested for study in this genus, clinical laboratory and clinicians: (1) Environmental study of this pathogen is important in each region (transfer to human from environmental source) (2) isolation of this microorganism from clinical samples is difficult and rarely because this microorganism are similar to Rhodococcus spp. and Nocardia spp. in some features and need a skillful specialist and molecular works.


The authors would like to thank Tehran University of Medical Sciences (school of public health) and Shahid Sadoughi University of Medical Sciences for their support.

Financial support and sponsorship


Conflicts of interest

There are no conflicts of interest.

  References Top

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Lai CC, Hsieh JH, Tsai HY, Liao CH, Hsueh PR. Cutaneous infection caused by Gordonia amicalis after a traumatic injury. J Clin Microbiol 2012;50:1821-2.  Back to cited text no. 2
Tsukamura M. Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. J Gen Microbiol 1971;68:15-26.  Back to cited text no. 3
Herath H, Athukoralage P, Jamie JF. Two oleanane triterpenoids from Gordonia ceylanica and their conversions to taraxarane triterpenoids. Phytochemistry 2000;54:823-7.  Back to cited text no. 4
Drancourt M, McNeil MM, Brown JM, Lasker BA, Maurin M, Choux M, et al. Brain abscess due to Gordona terrae in an immunocompromised child: Case report and review of infections caused by G. terrae. Clin Infect Dis 1994;19:258-62.  Back to cited text no. 5
Drancourt M, Pelletier J, Cherif AA, Raoult D. Gordona terrae central nervous system infection in an immunocompetent patient. J Clin Microbiol 1997;35:379-82.  Back to cited text no. 6
Lesens O, Hansmann Y, Riegel P, Heller R, Benaissa-Djellouli M, Martinot M, et al. Bacteremia and endocarditis caused by a Gordonia species in a patient with a central venous catheter. Emerg Infect Dis 2000;6:382-5.  Back to cited text no. 7
Zardawi IM, Jones F, Clark DA, Holland J. Gordonia terrae-induced suppurative granulomatous mastitis following nipple piercing. Pathology 2004;36:275-8.  Back to cited text no. 8
Nawaz SZ, Miles J, Skinner JA. Gordonia terrae causing metatarsal osteomyelitis in an immunocompetent patient: A case report. Eur Orthop Traumatol 2010;1:139-41.  Back to cited text no. 9
Habibnia S, Rasouli Nasab M, Heidarieh P, Bafghi MF, Pourmand M, Eshraghi S. Phenotypic characterization of Nocardia spp. isolated from Iran soil microflora. Int J Environ Health Eng 2015;4:20.  Back to cited text no. 10
Andalibi F, Bafghi MF, Heidarieh P, Nasab MR, Habibnia S, Pourmand MR, et al. Isolation and identification of Nocardia spp. using phenotypic methods from soil samples of North Khorasan province. J Med Bacteriol 2015;4:8-14.  Back to cited text no. 11
Rasouli Nasab M, Habibnia S, Heidarieh P, Pourmand M, Fatahi M, Eshraghi S. Comparison of paraffin bait, humic acid Vitamin B agar and paraffin agar methods to isolate Nocardia from soil. Med Lab J 2014;7:29-36.  Back to cited text no. 12
Bafghi MF, Eshraghi SS, Heidarieh P, Habibnia S, Rasouli Nasab M. DNA extraction from Nocardia species for special genes analysis using PCR. N Am J Med Sci 2014;6:231-3.  Back to cited text no. 13
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Goodfellow M, Alderson G. The actinomycete-genus Rhodococcus: A home for the “rhodochrous” complex. J Gen Microbiol 1977;100:99-122.  Back to cited text no. 15
Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997;47:479-91.  Back to cited text no. 16
Siddiqui N, Toumeh A, Georgescu C. Tibial osteomyelitis caused by Gordonia bronchialis in an immunocompetent patient. J Clin Microbiol 2012;50:3119-21.  Back to cited text no. 17
Werno AM, Anderson TP, Chambers ST, Laird HM, Murdoch DR. Recurrent breast abscess caused by Gordonia bronchialis in an immunocompetent patient. J Clin Microbiol 2005;43:3009-10.  Back to cited text no. 18
Blanc V, Dalle M, Markarian A, Debunne MV, Duplay E, Rodriguez-Nava V, et al. Gordonia terrae: A difficult-to-diagnose emerging pathogen? J Clin Microbiol 2007;45:1076-7.  Back to cited text no. 19
Gil-Sande E, Brun-Otero M, Campo-Cerecedo F, Esteban E, Aguilar L, García-de-Lomas J. Etiological misidentification by routine biochemical tests of bacteremia caused by Gordonia terrae infection in the course of an episode of acute cholecystitis. J Clin Microbiol 2006;44:2645-7.  Back to cited text no. 20
Lai CC, Wang CY, Liu CY, Tan CK, Lin SH, Liao CH, et al. Infections caused by Gordonia species at a medical centre in Taiwan, 1997 to 2008. Clin Microbiol Infect 2010;16:1448-53.  Back to cited text no. 21
Sng LH, Koh TH, Toney SR, Floyd M, Butler WR, Tan BH. Bacteremia caused by Gordonia bronchialis in a patient with sequestrated lung. J Clin Microbiol 2004;42:2870-1.  Back to cited text no. 22
Jannat-Khah DP, Halsey ES, Lasker BA, Steigerwalt AG, Hinrikson HP, Brown JM. Gordonia araii infection associated with an orthopedic device and review of the literature on medical device-associated Gordonia infections. J Clin Microbiol 2009;47:499-502.  Back to cited text no. 23
Steingrube VA, Wilson RW, Brown BA, Jost KC Jr., Blacklock Z, Gibson JL, et al. Rapid identification of clinically significant species and taxa of aerobic actinomycetes, including Actinomadura, Gordona, Nocardia, Rhodococcus, Streptomyces, and Tsukamurella isolates, by DNA amplification and restriction endonuclease analysis. J Clin Microbiol 1997;35:817-22.  Back to cited text no. 24
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  [Figure 1]

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