Antifungal activity of terrestrial Streptomyces rochei strain HF391 against clinical azole -resistant Aspergillus fumigatus


1 Department of Medical Mycology & Parasitology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran

2 Herbal and Traditional Medicines Research Center, Kerman University of Medical Sciences, Kerman, Iran

3 Department of Plant Pathology & Biotechnology, College of Agriculture, Bahonar University of Kerman, Iran

4 Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran


Background and Purpose: Actinomycetes have been discovered as source of antifungal compounds that are currently in clinical use. Invasive aspergillosis (IA) due to Aspergillus fumigatus has been identified as individual drug-resistant Aspergillus spp. to be an emerging pathogen opportunities a global scale. This paper described the antifungal activity of one terrestrial actinomycete against the clinically isolated azole-resistant A. fumigatus. Materials and Methods: Soil samples were collected from various locations of Kerman, Iran. Thereafter, the actinomycetes were isolated using starch-casein-nitrate-agar medium and the most efficient actinomycetes (capable of inhibiting A. fumigatus) were screened using agar block method. In the next step, the selected actinomycete was cultivated in starch-casein- broth medium and the inhibitory activity of the obtained culture broth was evaluated using agar well diffusion method. Results: The selected actinomycete, identified as Streptomyces rochei strain HF391, could suppress the growth of A. fumigatus isolates which was isolated from the clinical samples of patients treated with azoles. This strain showed higher inhibition zones on agar diffusion assay which was more than 15 mm. Conclusion: The obtained results of the present study introduced Streptomyces rochei strain HF391 as terrestrial actinomycete that can inhibit the growth of clinically isolated A. fumigatus.



Among the human pathogenic species of Aspergillus, A. fumigatus is perhaps the most devastating of Aspergillus-related diseases, followed by A. flavus, A. terreus, A. niger, and the model organism, A. nidulans [1-2]. Aspergillus fumigatus is a ubiquitous saprophytic mold that forms airborne spores (conidia). Humans inhale, on average, hundreds of these infectious propagules daily [3] .A. fumigatus pathogenesis and progression are the result of both fungal growth and the host response [4]. Invasive aspergillosis (IA) can cause a wide range of human ailments depending on host immune function [5]. Pathogenesis and virulence of aspergillus occurs when the host response is either too strong or too weak [6]. The types of hosts that are susceptible to invasive aspergillosis are the leukemic patients; hematopoietic stem cell transplant recipients, leukemia; patients on prolonged corticosteroid therapy, which is commonly utilized for the prevention and/or treatment of graft-versus-host disease in transplant patients; individuals with genetic immunodeficiencies such as chronic granuloma-tous disease (CGD); and individuals infected with human immunodeficiency virus [7]. In these patients, resistance is most commonly observed in A.fumigatus, and the isolates may be resistant to only itraconazole (ITZ) or exhibit a multi-azole or panazole–resistant phenotype. The phenotype depends on the underlying resistance mechanism, which commonly involves point mutations in the cyp51A-gene, the target for antifungal azoles [8]. In recent years the microorganisms have become important in the study of novel active compounds, secondary metabolites and chemical structure exhibiting antimicrobial may serve as model system in the discovery of new drugs [9]. The use of chemical fungicides has led to deteriorating human health and development of pathogen resistance to fungicide. Actinomycetes are the main source of antifungal. The antagonistic activity of actinomycetes is used for the bio-control of fungal diseases [10]. Actinomycetes produce about 75% of commercially and medically useful antibiotics [11-12]. Thus, the search for new antibiotics from these bacteria has gained importance. For example, it had been discovered in Egypt that a strain of Streptomyc-es spp., produced a strong antifungal antibiotics [13]. Furthermore, a research in Turkey for an antibacterial agent, producing Streptomyces spp. [14] and in China, a new strain of Streptomyces was discovered that kills certain pathogenic fungi [15].

Among the different types of drugs, secondary metabolites of actinomycetes including antibiotics with diverse chemical structure and biological activities have occupied a prominent position in the pharmaceutical industry [16]. This study was explored for the isolation characterization of native actinomyce-tes for antifungal metabolites, to screen a new antifungal compound against drug resistant A.fumigatus.

Material and Methods

Fungal strains

In the current study, an azole-resistant strain (IFRC 500, Invasive fungi Research Center, Mazandaran University of Medical Sciences), previously isolated from Bronchoalveolar Lavage (BAL) and identified by molecular methods were used. The resistant strain harbored an L98H amino acid substitution and a 34-bp tandem repeat in the cyp51A gene promoter region, and exhibited an itraconazole minimum inhibitory concentration (MIC) of > 16 µg/ml. Stock cultures for the transient working collections were cultured on malt extract agar (MEA, Difco, Beckton, Dickinson, and Company, Franklin Lakes, NJ, USA) at 35°C for 48 h until use.

Collection of soil samples

100 soil samples were collected from different points of Kerman City, Iran. The samples were taken up to a depth of 20 cm after removing approximately 3 cm of the soil surface and the samples were placed in polyethylene bags to avoid external contamination and kept in 4°C until pretreatment.

Isolation of actinomycetes

For the isolation of actinomycetes, various methods were performed on the basis of different sources and media [17]. Soil samples were processed by serial dilution method and cultured by spread plate technique on starch-casein-agar (SCB) and incubated at 37°C for 2 weeks. Slants containing pure cultures were stored at 4°C until further examination [18].

Identification of active actinomycetes

Various levels for the identification of actinomycetes were used such as: i) Chemo-taxonomical level: identified based on chemical variation and characters in all genera of actinomyces. ii) Classical level: identified based on macroscopic and microscopic methods and other properties such as the color of colonies culture. iii) Molecular level: the 16S rRNA partial gene sequences obtained from active isolate compared with other bacterial sequences by using PubMed - NCBI BLAST search [17].

Screening of the antifungal activity

Spread-plate method

The antifungal activity of actinomycetes was tested by agar plug method [19]. For the actinomycetes grown on surface of SCB medium Petri dishes, agar discs were cut out and transferred to the surface of PDA plates seeded with azole-resistant A.fumigatus. The petri dishes were incubated at 25°C to allow the growth of test organisms.

Well Diffusion Method

The isolated strains were transferred into the CG (Casein-Glycerin) medium in a 250 ml flask and incubated at 25°C for 15 days. Wells were made in the center of PDA plates seeded with Azole-resistant A. fumigatus. 100 μl of the test samples were transferred into the wells and plates were incubated at 25°C. The plates were then observed for zone of inhibition.

Assay for antifungal activity by minimum inhibitory concentration (MIC)

MIC was determined by the antimicrobial concentrations which were prepared as 1.25, 2.5, 5, 10, 20, 40 and 80 mg/ml in DMSO: MeOH (1:1, v/v) and tested in well-method technique against the pathogen. The lowest concentration which indicated growth inhibition was selected as MIC [18].


Identification of Azole-resistant A. fumigatus

Of the 50 Aspergillus isolates, 40 (80%) were Aspergillus fumigatus , of which one A.

drugs by agar well diffusion method (CLSI M38-A2) (Figure 1).

Chemicals Active strain
Citrate +
MR +
VP +
lactase test +
Proteases test +
ketones test -
Test for utilization of carbon sources
Carbon sources Active strain
Glucose +
Sucrose +
Maltose +
Mannitol +
Lactose +
Starch +
Growth in different temperature, osmolarity NaCl and pH
OsmolarityNaCl Growth Temperature Growth pH Growth
2/5 + 25 + 5 -
5 + 37 + 5/5 +
7/5 + 50 - 7/7 +
9/5 - - 7/8 +
12/5 - - 7/9 +
- - 8 +
- - 8/5 -
+, presence of growth; -, no growth
Table 1.Identification of strains by chemotaxonomical level

Identification of active strains

The active strain was identified by chemo- taxonomical level as well as the classical level. Results are shown in Tables 1 and 2.

Molecular level

Blast search for the 16S rRNA gene sequences of the isolates KP137826.1 in the NCBI data bank showed a maximum similarity of 86% with Streptomyces rochei strain HF391.

Actinomyces spp. kp137826 alone showed significant strong antifungal activity against the azoles-resistant A.fumigatus. The diameter of the zone of complete inhibition was measured to the nearest millimeter. Antibiotic production was not detected in 7 days culture filtrate, but that showed maximum antibiotic production after 9 days of incubation (Figure 2).

Minimum Inhibitory Concentration (MIC) determination

The best concentrations of the pure antifungal compounds from the Streptomyces rochei strain HF391 against azole-resistant A. fumigatus was 80 mg/ml. Furthermore, the inhibition zone (35mm) was measured as well (Figure 3).

Morphological Characteristics Active strain
Color of aerial mycelium Grey
Reverse side colour Pale Grey
Colony surface Smooth
Growth Good
Table 2.Identification of strains by Classical level

Figure 1.Colony of azole -resistant A. fumigatus on PDA medium

Figure 2.Zone of inhibition of Actinomyces spp. kp137826 (mm) against A.fumigatus


In our study, among fifty BAL samples, only one azoles (Clotrimazole, Itraconazole and Ketoconazole) -resistant A. fumigatus was found. In another study investigated the prevalence of azole-resistant Aspergillus spp. Only 4 azole-resistant isolates were found, which corresponds with a prevalence of 1.9% [20]. Another study showed the prevalence of 12.8% among A. fumigatus isolates that had been sent to hospitals in the Netherlands [21]. For patients with aspergillosis affected by azoles resistance A. fumigatus treated with voriconazole, the propor-tion of death was 48%

[22]. Another study investigated the prevalence of azole-resistant Aspergillus spp, described the emergence of acquired resistance of A. fumigatus to azole compounds [23].

In our research, among the 100 actinomycete isolates, Actinomyces spp. kp137826, exhibited strong antifungal activity against azole-resistant A. fumigatus. The rate of antifungal metabolite production correlated with the growth rate of the Actinomyces spp. kp137826. Among the bacteria, actinomycetes are the important source of bioactive compounds and many clinically relevant antibiotics in use today and may continue to be so. The other study performed on 153 isolates showed broad spectrum antifungal activity [24]. Augustine reported that out of 335 isolates, 230 (69 %) isolates were active against bacteria, fungi and yeast [25]. Of the 312 Actinomycete strains from different regions, of which, 22% exhibited antifungal activity against fungi [26]. Michael et al. and Gomeset al. isolated chitinolytic actinomycetes and found its antifungal activity [27-28].

Figure 3.Minimum inhibitory concentration (MIC) values of the culture supernatant of Actinomyces spp. kp137826 against A. fumigatus

Our study shows that only Actinomyces spp. kp137826 exhibited antifungal activity against azoles-resistance A. fumigatus. The MIC of the antifungal compound was determined as 80 mg/ml and showed the highest zone of inhibition A. fumigatus (35 mm). The other study used also different concentrations e.g. 2, 4, 6, and 10% of extract were used to check antifungal activity and the minimum inhibitory concentration [29].

Streptomyces spp and Nocardia spp. also showed anti-Aspergillus activity because of observed in Netherlands in 1999 [30].Screened287 isolates from various habitats and recorded166, 164, 134, and 132 actinomycete isolates active against C. albicans, A. niger, M. gypseum and T. rubrum,respectively [33]. In another research, among 316 actinomycetes, 19, 67, 42, 37, 18 and 25 isolates showed activity against C. albicans, T. rubrum, M. canis, M. gyseum, A. flavus, A. fumigatus, respectively [34]. Streptomyces rochei AK 39 also exhibited antifungal activity against dermatophytes when grown on starch-casein agar (SCA) medium with pH 7 and 37°C [35]. Several 32 [36]. In our study, we observed the antifungal activity of Actinomyces spp. actinomycetes were reported to possess anti-Aspergillus activity, e.g. Streptomyces spp. PM- kp137826 against A.fumigatus, enabling the discovery of new antibiotics and hence, merit future studies.


  1. Jaakkola MS, Ieromnimon A, Jaakkola JJ. Are atopy and specific IgE to mites and molds important for adult asthma?. J Allergy Clin Immunol. 2006; 117(3):642-8.
  2. Tao J, Segal BH, Eppolito C, Li Q, Dennis CG, Youn R. Aspergillusfumigatus extract differentially regulates antigen-specific CD4+ and CD8+ T cell responses to promote host immunity. J Leukoc Biol. 2006; 80(3):529-37.
  3. Li H, Zhou H, Luo H, Ouyang H, Hu H, Jin C. Glycosylphosphatidylinositol (GPI) anchor is required in Aspergillus fumigatus for morphogenesis and virulence. Mol Microbiol. 2007; 64(4):1014-27.
  4. Stephens-Romero S, Mednick AJ, Feldmesser M. The pathogenesis of fatal outcome in murine pulmonary aspergillosis depends on the neutrophil depletion strategy. Infect Immun. 2005; 73:114-25.
  5. Persat F, Noirey N, Diana J, Gariazzo MJ, Schmitt D, Vincent C. Binding of live conidia of Aspergillus fumigatus activates in vitro generated human Langerhans cells via a lectin of galactomannan specificity. Clin Exp Immunol. 2003; 133(3):370-7.
  6. Beck O, Topp U, Koehl E, Roilides M, Simitsopoulou M, Hanisch M. Generation of highly purified and functionally active human TH1 cells against Aspergillus fumigatus. Blood. 2006; 107(6):2562-9.
  7. Lin SJ, Schranz J, Teutsch SM. Aspergillosis case-fatality rate: systematic review of the literature. Clin Infect Dis. 2001; 32(3):358-66.
  8. Mellado E, Garcia-Effron G, Alcázar-Fuoli L, Melchers WJ, Verweij PE, Cuenca-Estrella M. A new Aspergillus fumigatus resistance mechanism conferring in vitro cross-resistance to azole antifungals involves a combination of cyp51A alterations. Antimicrob Agents Chemother. 2007; 51(6):1897-904.
  9. Newman DJ, Cragg GM. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Natu Prod. 2012; 75(3):311-35.
  10. Lim SW, Kim JD, Kim BS, Hwang BK. Isolation and numerical identification of Streptomyces humidus strain S5-55 antagonistic to plant pathogenic Fungi. Plant Pathol J. 2000; 16(4):189-99.
  11. Berdy J. Bioactive microbial metabolites. J Antibiot (Tokyo). 2005; 58(1):1-26.
  12. Miyadoh S. Research on antibiotic screening in Japan over the last decade: a producing microorganisms approach. Actinomycetol. 1993; 7(2):100-6.
  13. Atta HM. Production, purification, physicochemical characteristics and biological activities of antifungal antibiotic produced by streptomyces antibioticus, AZ-Z710. Am Eurasian J Sci Res. 2010; 5(1):39-49.
  14. Ceylan O, Okmen G, Ugur A. Isolation of soil Streptomyces as source antibiotics active against antibiotic-resistant bacteria. Eurasian J Bio Sci. 2008; 2(9):73-82.
  15. Jiang Y, Huang LL, Chen CQ, Qiao HP, Kang ZS. Screen, identification and optimized fermentation condition of an actinomycete strain against pathogenic fungus Fulviafulva. Wei Sheng Wu Xue Bao. 2007; 47(4):622-7.
  16. Raja A, Prabakarana P. Actinomycetes and drug-an overview. Am J Dru dis dev. 2011; 1(2):72-84.
  17. Sharma M. Actinomycetes: source, identification, and their applications. Int J Curr Microbiol App Sci. 2014; 3(2):801-32.
  18. Collins CH, Lyne PM, Granje JM. Microbiological methods. Butterworth and Heinemann Publishers: London; 1995.
  19. jayasree D, Tadikamal S, subba Rao CH, venkateshwar Rao J, Lakshmi NM. Enhancement of alkaline protease production isoloated from streptomyces pulveraceus using response surface methodology. Int J Pharm Pharm Sci. 2012; 4(3):226-31.
  20. Klaassen CH, de Valk HA, Curfs-Breuker IM, Meis JF. Novel mixed-format real-time PCR assay to detect mutations conferring resistance to triazoles in Aspergillus fumigatus and prevalence of multi-triazole resistance among clinical isolates in the Netherlands. J Antimicrob Chemother. 2010; 65(5):901-5.
  21. Van der Linden JW, Snelders E, Kampinga GA, Rijnders BJ, Mattsson E, Debets-Ossenkopp YJ. Clinical implications of azole resistance in Aspergillus fumigatus, the Netherlands, 2007–2009. Emerg Infect Dis. 2011; 17(10):1846-54.
  22. Baddley JW, Marr KA, Andes DR, Walsh TJ, Kauffman CA, Kontoyiannis DP. Patterns of susceptibility of Aspergillus isolates recovered from patients enrolled in the Transplant-Associated Infection Surveillance Network. J Clin Microbiol. 2009; 47(10):3271-5.
  23. Klaassen CH, de Valk HA, Curfs-Breuker IM, Meis JF. Novel mixed-format real-time PCR assay to detect mutations conferring resistance to triazoles in Aspergillus fumigatus and prevalence of multi-triazole resistance among clinical isolates in the Netherlands. J Antimicrob Chemother. 2010; 65(5):901-5.
  24. Basil AJ, Strap JL, Knotek-Smith HM, Crawford DL. Studies on the microbial population of the rhizosphere of big sagebrush (Artemisia tridentate). J Ind Microbiol Biotehnol. 2004; 31(6):278-88.
  25. Augustine SK, Bhavsar SP, Baserisalehi M, Kapadnis BP. Isolation, characterization and optimization of antifungal activtity of an actinomycete of soil origin. Indian J Exp Biol. 2004; 42(9):928-32.
  26. Jain PK, Jain PC. Antifungal activity of some actinomycetes isolated from various habitats. Hindustan Antibiot Bull. 2004; 45-46(1-4):5-10.
  27. Michael AP, Sommer MJ, Taras L. Bioactivity of chitinolyticactinomycetes of marine origin. Appl Microbiol Biotechnol. 1992; 36:553-5.
  28. Gomes RC, Semedo LT, Soares AM, Alviano CS, linhares LF, Coelho RR. Chitinolytic activity of actinomycetes from a cerrado soil and their potential in biocontrol. Lett Appl Microbiol. 2000; 30(2):146-50.
  29. Sharma H, Parihar L. Antifungal activity of extracts obtained from Actinomycetes. J Yeast Fungal Res. 2010; 1(10):197-200.
  30. Dhanasekaran D, Thajuddin N, Panneerselvam A. An Antifungal compound: 4' Phenyl -1-napthyl-phenyl acetamide from Streptomyces Sp DPTB16. Med Biol. 2008; 15(1):7-12.
  31. Ashadevi NK, Jeyarani M, Balakrishnan K. Isolation and identification of marine actinomycetes and their potential in antimicrobial activity. Pak J Biol Sci. 2006; 9(3):470-72.
  32. Wagner GH, Wolf DC. Principles and applications of soil microbiology. Pearson Prentice Hall USA; 1998.
  33. Sanasam S, Ningthoujam DS. Screening of local actinomycete isolates in Mnipur for anticandidal activity. Asian J Biotechnol. 2010; 2(2):139-45.
  34. Bharti A, Kumar V, Gusain O, Singh Bisht G. Antifungal Activity of Actinomycetes isolated from Garhwal Region. J Sci Engg Tech Mgt. 2010; 2(2):3-9.
  35. Augustine SK, Bhavsar SP, Kapadnis BP. Production of growth dependent metabolite activeagainst dermatophytes by Streptomyces rochei AK39. Indian J Med Res. 2005; 121(3):164-70.
  36. Manivasagan PS, Gnanam K, Sivakumar T, Thangaradjou S, Vijayalakshmi S, Balasubramanian T. Antimicrobial and cytotoxic ctivities of an actinobacteria(Streptomyces sp PM-32) Isolated from an offshore sediments of the Bay of Bengal in Tamilnadu. Adv Biol Res. 2009; 3(5-6):231-6.