First report of Gordonia terrae from Iran soil

Mehdi Fatahi-Bafghi; Fatemeh Andalibi; Seyyed Saeed Eshraghi

doi:10.4103/2277-9183.196667

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CASE REPORT

Int J Env Health Eng 2016, 5:24

First report of Gordonia terrae from Iran soil

Mehdi Fatahi-Bafghi¹, Fatemeh Andalibi², Seyyed Saeed Eshraghi²
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 Publication

26-Dec-2016

Correspondence Address:
Mehdi Fatahi-Bafghi
Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd
Iran

Source of Support: None, Conflict of Interest: None

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DOI: 10.4103/2277-9183.196667

Abstract

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: https://www.ijehe.org/text.asp?2016/5/1/24/196667

Introduction

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

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

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 (www.bacterio.net/gordonia.html). 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.

Acknowledgments

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

Nil.

Conflicts of interest

There are no conflicts of interest.

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