Something in the air: Actinomycetes, soil and facility contamination risk

Actinomycetes are a subgroup of the actinobacteria, Gram-positive organisms with a high guanine-cytosine (G+C) ratio in their DNA. This group is very old and appears to have branched off from the other groups early in the evolutionary sequence.

The actinomycete group includes many familiar and important bacteria, including Mycobacterium (the causal agents of tuberculosis and leprosy), Corynebacterium (a common commensal on human skin, and therefore often recovered in bacterial air samples), and Streptomyces (the source of many antibiotics as well as the odor of freshly turned soil, which relates to the release of a musty-smelling compound named 2-methylisoborneol and geosmin).

Some types of Actinomycetes can be detected in controlled environments. This is normally a sign of contamination control issues, such as transfer disinfection (or personnel movement (where contaminants may be transferred from footwear).

Bacterial profile

The actinomycetes are rod-shaped or filamentous. Those that are rod-shaped may form long, branching, chains of cells. Many actinomycetes form true filaments that branch and form colonies that look like fungi, although the diameter of the filaments is much smaller than that of the fungi. Filamentous forms produce spores that may be single, in short chains, or in very long chains that may form spirals.

In particular, Streptomyces resemble fungi in their life cycle. For example, during the vegetative growth stage of streptomycete development, DNA replication occurs without cellular division, creating a filamentous structure. Streptomyces reproduce and disperse through the formation of spores (conidia) which follow the period of vegetative growth. This is very similar to many fungi (1).

There are both anaerobic and aerobic actinomycetes. The truly filamentous forms are predominantly aerobic.

Ecology

Actinomycetes are abundant in soil and are responsible for much of the digestion of resistant carbohydrates such as chitin and cellulose. They are responsible for the freshly turned soil. Many actinomycetes and other actinobacteria are well-known as degraders of toxic materials and are used in bioremediation. They are particularly well adapted to survival in harsh environments. Some can grow at elevated temperatures (>50°C) and are essential to the composting process.

Fungal association

There is an interaction between actinomycetes and fungi, in that in the natural environment the two are often found in association. Therefore, when assessing contamination control it is not uncommon to find both in relation to the same event (2).

Interactions between Streptomyces and fungi trigger a mode of Streptomyces development. Streptomyces cells are ‘explorers’, using non-branching vegetative hyphal conformation to rapidly transverse solid surfaces. Fungi trigger Streptomyces exploratory growth in part by altering the composition of the growth medium. Streptomyces explorer cells can communicate this exploratory behavior to other physically separated streptomycetes using an airborne volatile organic compound (VOC). Hence, there is evidence of interkingdom interactions (3).

Human health

Antibiotics

Many antibiotics are produced by actinomycetes. These include novobiocin, amphotericin, vancomycin, neomycin, gentimycin, chloramphenicol, tetracycline, erythromycin, nystatin, and so on. Some of these antibiotics target bacterial ribosomes and are used in treating respiratory infections, including Legionnaires' disease (tetracycline, erythromycin). Vancomycin attacks bacterial cell walls and deadly organisms such as MRSA (methicillin-resistant Staphylococcus aureus) (multiply drug-resistant staph). Rifamycin targets bacterial RNA polymerase and is useful against tuberculosis and leprosy. Amphotericin is one of the few antibiotics that attack fungal membranes. These antibiotics generally do not affect human cells and therefore have few side effects. However, actinomycete metabolites such as adriamycin, prevent DNA replication and are used in the treatment of cancer, while rapamycin is used to suppress the immune system to enable organ transplants (4).

Infections

Members of the genus Actinomyces are normal commensal members of human oral cavities. They can cause serious infections when they invade tissues through breaks in the oral mucosa.

Nocardia steroids is an actinomycete that is common in soil and can cause infection via the respiratory route. Infection is opportunistic and relies on deficits in cell-mediated immunity. Other species of Nocardia may also be involved.

Hypersensitivity pneumonitis (HP)

Thermophilic actinomycetes are the most common cause of HP. Farmer’s lung disease is HP resulting from exposure to hay that has become colonized with thermophilic actinomycetes, which produce an abundance of airborne spores. Clouds of these spores are released when farmers (especially dairy farmers) handle stored hay in winter and early spring. The same fungi that cause molding of hay are common inhabitants of soil, and have also been documented to colonize ventilation systems, clothes dryers, refrigerator drip pans, and any other site that combines heat, cellulosic or other carbohydrate material, and water. Common species include Thermoactinomyces vulgaris, Saccharopolyspora rectivirgula, Thermoactinomyces viridis and others.

Volatile Organic Compounds (VOCs)

The odor of freshly turned soil is the result of geosmin, a volatile organic compound produced by actinomycetes. Geosmin is also produced by some cyanobacteria and produces an earthy taste in drinking water. Some fungi also produce geosmin, which can impart the same earthy taste to wine made from moldy grapes. In general, people find the geosmin odor pleasant in soil. However, one indoor air research group is investigating the possibility that exposure to geosmin is related to building-related symptoms. The data at present is too limited for conclusions. However, in the future, collection of samples that will reveal these organisms might be recommended.

Sampling and analysis

Generally, cultural sampling is necessary for the recovery of actinomycetes. Non-spore forming actinomycetes such as Corynebacterium are commonly recovered from air in human-occupied environments. These bacteria are carried on skin scales and thus are readily collected by most suction devices. Actinomyces species are fastidious and, thus not easy to culture and isolate. In general, they are relatively slow-growing.

Spore-forming actinomycetes are released into the air from environmental reservoirs as single or short chains of spores, and an efficient collector must be used. The particle size may be as small as 1 micron or less. The spores produced by these organisms are similar to endospores of Bacillus species and are resistant to environmental stresses. Actinomycete spores will germinate on the same culture media as other bacteria and are readily identified to the genus level. It is important to note that the thermophilic actinomycetes, while they grow on the same culture media as other bacteria, must be incubated at very high temperatures. Incubation temperatures in excess of 45°C are essential for the recovery of these organisms.

The spores of thermophilic actinomycetes are resistant to high temperatures. Spores appear more resistant to dry heat compared with moist heat. Spores can survive for six hours at 100°C dry heat (5).

What have we learned?

Actinomycetes have adapted to a wide range of environments, such as soil, water (even salty), and air, and hence they present a contamination control risk for the transfer of items into the facility (and perhaps via personnel). Some species are hardy and produce heat-resistant spores (6).

In terms of the greatest risk, the predominant number of these organisms are preferentially found in alkaline soil with big amounts of organic matter, making facilities in rural areas seemingly the most potentially vulnerable.

References

1. Chater, Keith F.; Biró, Sandor; Lee, Kye Joon; Palmer, Tracy; Schrempf, Hildgund (2010). The complex extracellular biology of Streptomyces. FEMS Microbiology Reviews. 34 (2): 171–98. Doi:10.1111/j.1574-6976.2009.00206.x

2. Sullivan, DC; Chapman, SW (2010) Bacteria that masquerade as fungi: actinomycosis/nocardia, Proc Am Thorac Soc, 7 (3): 216–221

3. Jones, S. E. et al Streptomyces exploration is triggered by fungal interactions and volatile signals, eLife, 2017, 6:e21738: https://elifesciences.org/articles/21738

4. Waksman, Selman A.; Schatz, Albert; Reynolds, Donald M. (2010). Production of antibiotic substances by Actinomycetes. Annals of the New York Academy of Sciences. 1213 (1): 112–124

5. Tendler, M. and Burkholder, P.  1961. Studies on the thermophilic actinomycetes. I. Methods of cultivation. Appl. Microbiol.9: 394–399

6. Barka E.A., Vatsa P., Sanchez L., Gaveau-Vaillant N., Jacquard C., Klenk H.-P., Clément C., Ouhdouch Y., van Wezel G.P. Taxonomy, physiology, and natural products of actinobacteria. Microbiol. Mol. Biol. R. 2016;80:1–43. doi: 10.1128/MMBR.00019-15