Microbiology is the branch of science that deals with microscopic, unicellular, and cell-cluster organisms. The major microbial categories that may be associated with eye infections are bacteria, viruses, fungi , and parasites . A basic understanding of microbiology is helpful for the ophthalmic assistant, who may be required to take smears, stain the appropriate slide, and assist in taking a culture.

In everyday life, we are constantly in touch with microbes. We wash our hands to lower the number of microbes on our outer skin. We disinfect wounds for the same reason. We cover our sneezes and wash our fruit to prevent getting or spreading infectious diseases. We add chlorine to our water supply to inhibit the growth of pathogenic (disease-causing) bacteria. We do many things to control the growth of bacteria, but most bacteria are helpful in our daily lives. In fact, we could not live without the help of certain bacteria that exist in and on our bodies. For example, bacteria in our gut are necessary for absorption of certain vitamins. Some bacteria actually educate our immune system and help to protect us against pathogenic microbial invaders. Certain species of bacteria are normal inhabitants of specific geographic areas of the body and their numbers are controlled by the local environment’s moisture, temperature, and available nutrients. However, when such bacteria (say from the gut) get into the wrong place (like the eye) they have the potential to cause disease.

The eye is subject to the same types of infections that may occur in other parts of the body. Microorganisms are everywhere in our environment, and fortunately the eye is very resistant to infection. Our intact epithelial skin surface resists most microbial invaders. Any break in the skin of the outer eye can act as a portal of entry for microbes, at which point if a significant concentration of microbes, an inoculum , is present it may overcome our ocular defenses and cause an infection. Ocular trauma, surgery, radiation, severe surface dryness from exposure or inadequate blinking, lid abnormalities, and corneal degenerative changes may create surface disruptions that leave the eye more susceptible to infection. Persons with normal ocular surface structures may still be susceptible to diseases if their ability to defend against infectious agents is compromised. A compromised immune system can be present in patients with diabetes, acquired immunodeficiency syndrome (AIDS), and those taking immunosuppressive agents, such as oral steroids.

A variety of organisms can cause ocular disease of the eye ( Box 5.1 ). These infectious agents have a predilection for certain sites of the eye and usually vary in their severity in causing ocular disease. By far the most common infections result from bacterial and viral organisms. Bacteria are larger than viruses and may easily be seen under magnification by a light microscope. Bacteria range in size from 0.2 to 5 μm and viruses from 0.005 to 0.1 μm. Viruses cannot be seen with a light microscope but can be indirectly viewed with electron microscopes.

Box 5.1

Common organisms causing disease in the anterior segment of the eye



Gram positive

  • Staphylococcus

  • Streptococcus

Gram negative

  • Gonococcus

  • Meningococcus


Gram negative

  • Pseudomonas

  • Haemophilus

  • Moraxella

Gram positive

  • Corynebacterium

  • Bacillus

  • Mycobacterium


  • Treponema (syphilis)


  • Herpes simplex

  • Herpes zoster

  • Adenovirus


  • Candida

  • Fusarium

  • Aspergillus


  • Chlamydia trachomatis


  • Acanthamoeba

  • Microsporidia


Bacteria can be categorized in different ways ( Fig. 5.1 ). They are commonly classified by morphology (shape), Gram character (dyed color), and ability to live in and use oxygen. Morphologically, there are three basic shapes: the round cocci , the rod-shaped bacilli , and the helix-shaped spirochetes ( Fig. 5.2 ). Although the shape can be used to classify the organism, another important differentiating feature is whether the organism stains blue (gram positive) or red (gram negative) with a special stain referred to as Gram stain . The organism’s color after Gram staining is referred to as its Gram character. A bacterium’s Gram character tells us about its cell wall makeup and therefore which antibiotics may be useful.

Fig. 5.1


Fig. 5.2

Gram stain showing gram-positive rods on the left (A) and gram-positive cocci on the right (B).

(Courtesy of Hans E. Grossniklaus, MD.)

The coccus is a round bacterium that arranges itself in a variety of patterns, each with its own characteristics. Certain strains of Staphylococcus spp., Streptococcus spp., and Neisseria spp. are sometimes referred to as pyogenic or pus-producing bacteria . Staphylococcus spp. are gram-positive organisms that may appear in grape-like clusters or, more commonly, singly or in pairs. Staphylococci frequently are present on the skin and may give rise to boils and styes. Not all staphylococci are pathogenic (disease causing); Staphylococcus epidermidis is a normal floral organism that lives on our skin and seldom causes disease. Staphylococcus aureus , however, is the species most commonly associated with skin infections. A particular type known as methicillin-resistant Staphylococcus aureus (MRSA) is a bacterium responsible for several difficult-to-treat infections in humans. It is increasingly reported as a pathogen in the skin and other tissue infections. Hospital-acquired MRSA infections are on the decline, but community-based MRSA infections are on the rise.

Streptococci are bullet-shaped gram-positive cocci that are usually arranged in pairs and short chains. Of the streptococcal organisms, the most common agent to affect the eye is Streptococcus pneumoniae (also known as Pneumococcus, Diplococcus ). When causing disease, this organism possesses a polysaccharide (slime) capsule. The encapsulated form of this organism protects it from our body’s defenses. Although Pneumococcus is a common cause of lobar pneumonia, it can also be the cause of conjunctivitis, a corneal ulcer, or an infection inside the eye referred to as endophthalmitis .

The bacterial genus Neisseria is a gram-negative cocci. The species Neisseria gonorrhoeae , also known as the gonococcus , and Neisseria meningitidis , also known as the meningococcus , are diplococci (paired) and have a characteristic kidney-bean shape. They are the causative agents of gonorrhea and meningitis, respectively. These organisms are very invasive and rapid in their destruction.

Another group of bacteria are the bacilli. All the members of this group are rod shaped, the rods being long or short, plump or slender, curved or straight, smooth or beaded. Commonly affecting the eye are the gram-negative rods, Haemophilus spp., Serratia spp., and Pseudomonas . Historically, the organism Pseudomonas aeruginosa has been considered the most devastating gram-negative bacillus because of its very rapid and destructive potential. Pseudomonas is an opportunistic pathogen. It cannot usually penetrate our intact skin and it causes disease only when given an opportunity, such as a corneal abrasion. It is the most common cause of corneal ulcers in patients wearing contact lenses. Unless treatment is initiated early, the organism can cause significant visual loss.

Gram-positive bacilli that affect the eye include Corynebacterium spp., Bacillus spp., and Mycobacterium spp. Corynebacteria are anaerobic rods that are part of our normal flora and live just beneath the outer skin layer. Bacillus spp. are soil organisms that seldom cause disease but are devastating in their destruction when involved in intraocular infections. Mycobacterial keratitis is rare but is often associated with previous ocular surgery. It is very difficult to treat and often results in poor visual outcomes.

The third group, the spiral-shaped organisms as found in Treponema pallidum , comprises small organisms whose diameter is below the range of resolution of the routine light microscope and which are rarely associated with ocular disease.

The positive identification of bacterial organisms by microscopic shape and staining reaction alone is not usually possible, and culture characteristics are often necessary. The ophthalmologist, however, may frequently make a presumptive diagnosis in association with the clinical picture, but the microscopic picture always remains an important aid.


Viruses are very different from bacteria. They are made of the genetic material ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), never both, plus a bit of protein. They are obligate intracellular parasites that cannot live on their own. Viruses are very small organisms (5–300 nm) that are not visible through a light microscope. Viruses multiply by injecting their genetic material into suitable host cells. Once inside, they commandeer the reproductive machinery of the host cell and reprogram it to make more viruses.

Our bodies acquire immunity to most viruses during the course of a viral infection so we can fight off a repeat infection by the same strain of virus in the future. However, our bodies are not capable of immunity to all viruses, notably herpes simplex and human immunodeficiency virus (HIV). The herpes simplex virus lives dormant in the nerve ganglia and when activated travels along the nerve root to invade the corneal epithelium and may give rise to a dendritic (branching) or geographic corneal ulcer. The virus can be identified by scraping the advancing edge of the corneal ulcer and inoculating the specimen into a cell culture system. In most cases, however, the clinical diagnosis of herpes simplex virus is readily apparent and a scraping is unnecessary.

A common disease known as epidemic keratoconjunctivitis (EKC) is caused by an adenovirus . Adenoviruses are highly contagious and may affect the upper respiratory tract, the conjunctiva, and the cornea, causing fever, lymph gland enlargement, conjunctivitis, and keratitis. Varicella z oster virus causes chickenpox in children and is responsible for causing a vesicular eruption on the skin referred to as shingles in adults. It resides in the trigeminal nerve ganglion (CN-V) and is therefore restricted to only one side of the face, stopping at the midline. Some patients may develop ocular involvement that most commonly manifests as keratitis or iritis.

Coronavirus, SARS-CoV-2, causes the infectious disease COVID-19, which is a respiratory pathogen. The World Health Organization first learned of this new virus from cases in Wuhan, People’s Republic of China on 31 December 2019, which later resulted in spread of the virus and a worldwide pandemic. The virus can cause a conjunctivitis in addition to affecting many organs of the body.


Fungal ocular infections are much less common than bacterial and viral infections. Molds and mildew are fungi. Athlete’s foot and ringworm are two common skin diseases caused by fungi. Fungi are larger than bacteria and grow either as a mass of branching interlacing filaments ( Fig. 5.3 ) or as rounded yeast forms. They are typically found in soil and moist environments.

Fig. 5.3

Gram stain of Fusarium sp. fungi.

Ocular fungal infections are more likely to occur in the outer eye, cornea, and occasionally in the lacrimal sac. Ocular mycoses (fungal infections) are typically associated with trauma involving plant matter. A typical history is one in which a patient’s cornea is scratched by a twig or leaf, and several days later the eye becomes red and inflamed. The most common fungal infection of the eye is caused by Candida albicans ( Fig. 5.4 ), which is a common yeast that also grows on moist skin and on mucous membranes as normal flora, but may overgrow and cause disease. Other fungi that may cause eye infections are the branching fungi Aspergillus spp. and Fusarium spp., both being more common in warm and moist climates. The largest outbreak of fungal keratitis ever recorded occurred in 2006; it was caused by a Fusarium sp. and was associated with a newly introduced contact lens multipurpose lens care product.

Fig. 5.4

Candida albicans . Note both yeast and hyphae.

Other microbes

Chlamydial organisms are technically classified as bacteria but deserve a classification of their own. They are intracellular parasites that are larger than viruses but smaller than most bacteria. Chlamydia is the most widespread sexually transmitted bacterial disease in the United States. In North America the most common chlamydial eye disease is adult inclusion keratoconjunctivitis, which is usually spread from an infected sexual partner. Chlamydia may be transferred to infants while passing through the birth canal and result in an eye infection called ophthalmia neonatorum (eye disease of the newborn). Outside of North America, (in North Africa, the Middle East, and South Asia), another chlamydial disease, trachoma, remains epidemic and a serious cause of ocular morbidity. Diagnosis of inclusion keratoconjunctivitis can be made by obtaining a scraping of the conjunctiva and looking for inclusion bodies (microscopic foreign particles) in the cytoplasm of the epithelial cells. In infant chlamydial disease, the probability of finding inclusion bodies is higher than in adults. A culture or specialized immunofluorescent test can also be used to confirm the diagnosis.

Protozoa are small single-celled parasites that eat organic matter including bacteria and infrequently may cause ocular infections. Acanthamoeba and Microsporidia are two protozoa capable of affecting the eye. Acanthamoeba can cause significant ocular morbidity. The organism is ubiquitous; it can be found in freshwater, soil, swimming pools, and hot tubs. It is capable of causing keratitis, which can progress despite the best available medication. Unhygienic contact lens use is the major risk factor for acquiring this infection; it feeds on bacteria in the contact lens case. This risk is increased when wearers use homemade saline, rinse lenses with tap water, or swim while wearing contact lenses. Corneal transplantation may be required to restore vision but unfortunately there is approximately a 30% recurrence rate of the parasite in the graft. Microsporidia are small simple single-celled parasites that may infect compromised hosts. They are most commonly found in HIV-positive individuals and occasionally in other compromised hosts, such as those on prolonged steroid use. They are too small to be seen by simple light microscopy but may be detected by immunoassay or electron microscopy.

Bacteria, viruses, fungi, chlamydia, and parasites are among the causes of infectious inflammations of various parts of the human body, including the eye. Various terms are used to denote the specific site of inflammation, as noted in Table 5.1 . Each part of the eye is susceptible to attack by a large variety of organisms that have in common a predisposition to attack these specific areas.

Jun 26, 2022 | Posted by in OPHTHALMOLOGY | Comments Off on Microbiology
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