Anatomy and Microbiota of the Eye

Although the eye and skin have distinct anatomy, they are both in direct contact with the external environment. An important component of the eye is the nasolacrimal drainage system, which serves as a conduit for the fluid of the eye, called tears. Tears flow from the external eye to the nasal cavity by the lacrimal apparatus, which is composed of the structures involved in tear production (Figure 21.6). The lacrimal gland, above the eye, secretes tears to keep the eye moist. There are two small openings, one on the inside edge of the upper eyelid and one on the inside edge of the lower eyelid, near the nose. Each of these openings is called a lacrimal punctum. Together, these lacrimal puncta collect tears from the eye that are then conveyed through lacrimal ducts to a reservoir for tears called the lacrimal sac, also known as the dacrocyst or tear sac.

From the sac, tear fluid flows via a nasolacrimal duct to the inner nose. Each nasolacrimal duct is located underneath the skin and passes through the bones of the face into the nose. Chemicals in tears, such as defensinslactoferrin, and lysozyme, help to prevent colonization by pathogens. In addition, mucins facilitate removal of microbes from the surface of the eye.

Figure 21.6 The lacrimal apparatus includes the structures of the eye associated with tear production and drainage. (credit: modification of work by “Evidence Based Medical Educator Inc.”/YouTube)

The surfaces of the eyeball and inner eyelid are mucous membranes called conjunctiva. The normal conjunctival microbiota has not been well characterized, but does exist. One small study (part of the Ocular Microbiome project) found twelve genera that were consistently present in the conjunctiva. These microbes are thought to help defend the membranes against pathogens. However, it is still unclear which microbes may be transient and which may form a stable microbiota.

Use of contact lenses can cause changes in the normal microbiota of the conjunctiva by introducing another surface into the natural anatomy of the eye. Research is currently underway to better understand how contact lenses may impact the normal microbiota and contribute to eye disease.

The watery material inside of the eyeball is called the vitreous humor. Unlike the conjunctiva, it is protected from contact with the environment and is almost always sterile, with no normal microbiota (Figure 21.7).

Figure 21.7 Some microbes live on the conjunctiva of the human eye, but the vitreous humor is sterile.

Infections of the Eye

The conjunctiva is a frequent site of infection of the eye; like other mucous membranes, it is also a common portal of entry for pathogens. Inflammation of the conjunctiva is called conjunctivitis, although it is commonly known as pinkeye because of the pink appearance in the eye. Infections of deeper structures, beneath the cornea, are less common (Figure 21.8). Conjunctivitis occurs in multiple forms. It may be acute or chronic. Acute purulent conjunctivitis is associated with pus formation, while acute hemorrhagic conjunctivitis is associated with bleeding in the conjunctiva. The term blepharitis refers to an inflammation of the eyelids, while keratitis refers to an inflammation of the cornea (Figure 21.8); keratoconjunctivitis is an inflammation of both the cornea and the conjunctiva, and dacryocystitis is an inflammation of the lacrimal sac that can often occur when a nasolacrimal duct is blocked.

Figure 21.8 (a) Conjunctivitis is inflammation of the conjunctiva. (b) Blepharitis is inflammation of the eyelids. (c) Keratitis is inflammation of the cornea. (credit a: modification of work by Lopez-Prats MJ, Sanz Marco E, Hidalgo-Mora JJ, Garcia-Delpech S, Diaz-Llopis M; credit b, c: modification of work by Centers for Disease Control and Prevention)

Infections leading to conjunctivitis, blepharitis, keratoconjunctivitis, or dacryocystitis may be caused by bacteria or viruses, but allergens, pollutants, or chemicals can also irritate the eye and cause inflammation of various structures. Viral infection is a more likely cause of conjunctivitis in cases with symptoms such as fever and watery discharge that occurs with upper respiratory infection and itchy eyes. Table 21.2 summarizes some common forms of conjunctivitis and blepharitis.

Types of Conjunctivities and Blepharitis
Condition Description Causative Agent(s)
Acute purulent conjunctivitis Conjunctivitis with purulent discharge Bacterial (HaemophilusStaphylococcus)
Acute hemorrhagic conjunctivitis Involves subconjunctival hemorrhages Viral (Picornaviradae)
Acute ulcerative blepharitis Infection involving eyelids; pustules and ulcers may develop Bacterial (Staphylococcal) or viral (herpes simplex, varicella-zoster, etc.)
Follicular conjunctivitis Inflammation of the conjunctiva with nodules (dome-shaped structures that are red at the base and pale on top) Viral (adenovirus and others); environmental irritants
Dacryocystitis Inflammation of the lacrimal sac often associated with a plugged nasolacrimal duct Bacterial (Haemophilus, StaphylococcusStreptococcus)
Keratitis Inflammation of cornea Bacterial, viral, or protozoal; environmental irritants
Keratoconjunctivitis Inflammation of cornea and conjunctiva Bacterial, viral (adenoviruses), or other causes (including dryness of the eye)
Nonulcerative blepharitis Inflammation, irritation, redness of the eyelids without ulceration Environmental irritants; allergens
Papillary conjunctivitis Inflammation of the conjunctiva; nodules and papillae with red tops develop

Table 21.2

Bacterial Eye Infections

Bacterial Conjunctivitis

Like the skin, the surface of the eye comes in contact with the outside world and is somewhat prone to infection by bacteria in the environment. Bacterial conjunctivitis (pinkeye) is a condition characterized by inflammation of the conjunctiva, often accompanied by a discharge of sticky fluid (described as acute purulent conjunctivitis) (Figure 21.21). Conjunctivitis can affect one eye or both, and it usually does not affect vision permanently. Bacterial conjunctivitis is most commonly caused by Haemophilusinfluenzae, but can also be caused by other species such as Moraxella catarrhalisS. pneumoniae, and S. aureus. The causative agent may be identified using bacterial cultures, Gram stain, and diagnostic biochemical, antigenic, or nucleic acid profile tests of the isolated pathogen. Bacterial conjunctivitis is very contagious, being transmitted via secretions from infected individuals, but it is also self-limiting. Bacterial conjunctivitis usually resolves in a few days, but topical antibiotics are sometimes prescribed. Because this condition is so contagious, medical attention is recommended whenever it is suspected. Individuals who use contact lenses should discontinue their use when conjunctivitis is suspected. Certain symptoms, such as blurred vision, eye pain, and light sensitivity, can be associated with serious conditions and require medical attention.

Figure 21.21Acute, purulent, bacterial conjunctivitis causes swelling and redness in the conjunctiva, the membrane lining the whites of the eyes and the inner eyelids. It is often accompanied by a yellow, green, or white discharge, which can dry and become encrusted on the eyelashes. (credit: “Tanalai”/Wikimedia Commons)

Neonatal Conjunctivitis

Newborns whose mothers have certain sexually transmitted infections are at risk of contracting ophthalmia neonatorum or inclusion conjunctivitis, which are two forms of neonatal conjunctivitis contracted through exposure to pathogens during passage through the birth canal. Gonococcal ophthalmia neonatorum is caused by Neisseria gonorrhoeae, the bacterium that causes the STD gonorrhea (Figure 21.22). Inclusion (chlamydial) conjunctivitis is caused by Chlamydia trachomatis, the anaerobic, obligate, intracellular parasite that causes the STD chlamydia.

To prevent gonoccocal ophthalmia neonatorum, silver nitrate ointments were once routinely applied to all infants’ eyes shortly after birth; however, it is now more common to apply antibacterial creams or drops, such as erythromycin. Most hospitals are required by law to provide this preventative treatment to all infants, because conjunctivitis caused by N. gonorrhoeaeC. trachomatis, or other bacteria acquired during a vaginal delivery can have serious complications. If untreated, the infection can spread to the cornea, resulting in ulceration or perforation that can cause vision loss or even permanent blindness. As such, neonatal conjunctivitis is treated aggressively with oral or intravenous antibiotics to stop the spread of the infection. Causative agents of inclusion conjunctivitis may be identified using bacterial cultures, Gram stain, and diagnostic biochemical, antigenic, or nucleic acid profile tests.

Figure 21.22A newborn suffering from gonoccocal opthalmia neonatorum. Left untreated, purulent discharge can scar the cornea, causing loss of vision or permanent blindness. (credit: Centers for Disease Control and Prevention)


Trachoma, or granular conjunctivitis, is a common cause of preventable blindness that is rare in the United States but widespread in developing countries, especially in Africa and Asia. The condition is caused by the same species that causes neonatal inclusion conjunctivitis in infants, Chlamydia trachomatisC. trachomatis can be transmitted easily through fomites such as contaminated towels, bed linens, and clothing and also by direct contact with infected individuals. C. trachomatis can also be spread by flies that transfer infected mucous containing C. trachomatis from one human to another.

Infection by C. trachomatis causes chronic conjunctivitis, which leads to the formation of necrotic follicles and scarring in the upper eyelid. The scars turn the eyelashes inward (a condition known as trichiasis) and mechanical abrasion of the cornea leads to blindness (Figure 21.23). Antibiotics such as azithromycin are effective in treating trachoma, and outcomes are good when the disease is treated promptly. In areas where this disease is common, large public health efforts are focused on reducing transmission by teaching people how to avoid the risks of the infection.

Figure 21.23 (a) If trachoma is not treated early with antibiotics, scarring on the eyelid can lead to trichiasis, a condition in which the eyelashes turn inward. (b) Trichiasis leads to blindness if not corrected by surgery, as shown here. (credit b: modification of work by Otis Historical Archives National Museum of Health & Medicine)

Micro Connections

SAFE Eradication of Trachoma

Though uncommon in the United States and other developed nations, trachoma is the leading cause of preventable blindness worldwide, with more than 4 million people at immediate risk of blindness from trichiasis. The vast majority of those affected by trachoma live in Africa and the Middle East in isolated rural or desert communities with limited access to clean water and sanitation. These conditions provide an environment conducive to the growth and spread of Chlamydia trachomatis, the bacterium that causes trachoma, via wastewater and eye-seeking flies.

In response to this crisis, recent years have seen major public health efforts aimed at treating and preventing trachoma. The Alliance for Global Elimination of Trachoma by 2020 (GET 2020), coordinated by the World Health Organization (WHO), promotes an initiative dubbed “SAFE,” which stands for “Surgery, Antibiotics, Facial cleanliness, and Environmental improvement.” The Carter Center, a charitable, nongovernment organization led by former US President Jimmy Carter, has partnered with the WHO to promote the SAFE initiative in six of the most critically impacted nations in Africa. Through its Trachoma Control Program, the Carter Center trains and equips local surgeons to correct trichiasis and distributes antibiotics to treat trachoma. The program also promotes better personal hygiene through health education and improves sanitation by funding the construction of household latrines. This reduces the prevalence of open sewage, which provides breeding grounds for the flies that spread trachoma.

Bacterial Keratitis

Keratitis can have many causes, but bacterial keratitis is most frequently caused by Staphylococcus epidermidis and/or Pseudomonas aeruginosa. Contact lens users are particularly at risk for such an infection because S. epidermidis and P. aeruginosa both adhere well to the surface of the lenses. Risk of infection can be greatly reduced by proper care of contact lenses and avoiding wearing lenses overnight. Because the infection can quickly lead to blindness, prompt and aggressive treatment with antibiotics is important. The causative agent may be identified using bacterial cultures, Gram stain, and diagnostic biochemical, antigenic, or nucleic acid profile tests of the isolated pathogen.

Biofilms and Infections of the Skin and Eyes

When treating bacterial infections of the skin and eyes, it is important to consider that few such infections can be attributed to a single pathogen. While biofilms may develop in other parts of the body, they are especially relevant to skin infections (such as those caused by S. aureus or P. aeruginosa) because of their prevalence in chronic skin wounds. Biofilms develop when bacteria (and sometimes fungi) attach to a surface and produce extracellular polymeric substances (EPS) in which cells of multiple organisms may be embedded. When a biofilm develops on a wound, it may interfere with the natural healing process as well as diagnosis and treatment.

Because biofilms vary in composition and are difficult to replicate in the lab, they are still not thoroughly understood. The extracellular matrix of a biofilm consists of polymers such as polysaccharides, extracellular DNA, proteins, and lipids, but the exact makeup varies. The organisms living within the extracellular matrix may include familiar pathogens as well as other bacteria that do not grow well in cultures (such as numerous obligate anaerobes). This presents challenges when culturing samples from infections that involve a biofilm. Because only some species grow in vitro, the culture may contain only a subset of the bacterial species involved in the infection.

Biofilms confer many advantages to the resident bacteria. For example, biofilms can facilitate attachment to surfaces on or in the host organism (such as wounds), inhibit phagocytosis, prevent the invasion of neutrophils, and sequester host antibodies. Additionally, biofilms can provide a level of antibiotic resistance not found in the isolated cells and colonies that are typical of laboratory cultures. The extracellular matrix provides a physical barrier to antibiotics, shielding the target cells from exposure. Moreover, cells within a biofilm may differentiate to create subpopulations of dormant cells called persister cells. Nutrient limitations deep within a biofilm add another level of resistance, as stress responses can slow metabolism and increase drug resistance.

Disease Profile

Bacterial Infections of the Eyes

A number of bacteria are able to cause infection when introduced to the mucosa of the eye. In general, bacterial eye infections can lead to inflammation, irritation, and discharge, but they vary in severity. Some are typically short-lived, and others can become chronic and lead to permanent eye damage. Prevention requires limiting exposure to contagious pathogens. When infections do occur, prompt treatment with antibiotics can often limit or prevent permanent damage. Figure 21.24 summarizes the characteristics of some common bacterial infections of the eyes.

Figure 21.24

Viral Eye Infections

Viral Conjunctivitis

Like bacterial conjunctivitis viral infections of the eye can cause inflammation of the conjunctiva and discharge from the eye. However, viral conjunctivitis tends to produce a discharge that is more watery than the thick discharge associated with bacterial conjunctivitis. The infection is contagious and can easily spread from one eye to the other or to other individuals through contact with eye discharge.

Viral conjunctivitis is commonly associated with colds caused by adenoviruses; however, other viruses can also cause conjunctivitis. If the causative agent is uncertain, eye discharge can be tested to aid in diagnosis. Antibiotic treatment of viral conjunctivitis is ineffective, and symptoms usually resolve without treatment within a week or two.

Herpes Keratitis

Herpes infections caused by HSV-1 can sometimes spread to the eye from other areas of the body, which may result in keratoconjunctivitis. This condition, generally called herpes keratitis or herpetic keratitis, affects the conjunctiva and cornea, causing irritation, excess tears, and sensitivity to light. Deep lesions in the cornea may eventually form, leading to blindness. Because keratitis can have numerous causes, laboratory testing is necessary to confirm the diagnosis when HSV-1 is suspected; once confirmed, antiviral medications may be prescribed.

Protozoan and Helminthic Infections of the Skin and Eyes

Many parasitic protozoans and helminths use the skin or eyes as a portal of entry. Some may physically burrow into the skin or the mucosa of the eye; others breach the skin barrier by means of an insect bite. Still others take advantage of a wound to bypass the skin barrier and enter the body, much like other opportunistic pathogens. Although many parasites enter the body through the skin, in this chapter we will limit our discussion to those for which the skin or eyes are the primary site of infection. Parasites that enter through the skin but travel to a different site of infection will be covered in other chapters. In addition, we will limit our discussion to microscopic parasitic infections of the skin and eyes. Macroscopic parasites such as lice, scabies, mites, and ticks are beyond the scope of this text.

Acanthamoeba Infections

Acanthamoeba is a genus of free-living protozoan amoebae that are common in soils and unchlorinated bodies of fresh water. (This is one reason why some swimming pools are treated with chlorine.) The genus contains a few parasitic species, some of which can cause infections of the eyes, skin, and nervous system. Such infections can sometimes travel and affect other body systems. Skin infections may manifest as abscesses, ulcers, and nodules. When acanthamoebae infect the eye, causing inflammation of the cornea, the condition is called Acanthamoeba keratitis. Figure 21.34 illustrates the Acanthamoeba life cycle and various modes of infection.

While Acanthamoeba keratitis is initially mild, it can lead to severe corneal damage, vision impairment, or even blindness if left untreated. Similar to eye infections involving P. aeruginosa, Acanthamoeba poses a much greater risk to wearers of contact lenses because the amoeba can thrive in the space between contact lenses and the cornea. Prevention through proper contact lens care is important. Lenses should always be properly disinfected prior to use, and should never be worn while swimming or using a hot tub.

Acanthamoeba can also enter the body through other pathways, including skin wounds and the respiratory tract. It usually does not cause disease except in immunocompromised individuals; however, in rare cases, the infection can spread to the nervous system, resulting in a usually fatal condition called granulomatous amoebic encephalitis (GAE). Disseminated infections, lesions, and Acanthamoeba keratitis can be diagnosed by observing symptoms and examining patient samples under the microscope to view the parasite. Skin biopsies may be used.

Acanthamoeba keratitis is difficult to treat, and prompt treatment is necessary to prevent the condition from progressing. The condition generally requires three to four weeks of intensive treatment to resolve. Common treatments include topical antiseptics (e.g., polyhexamethylene biguanidechlorhexidine, or both), sometimes with painkillers or corticosteroids (although the latter are controversial because they suppress the immune system, which can worsen the infection). Azoles are sometimes prescribed as well. Advanced cases of keratitis may require a corneal transplant to prevent blindness.

Figure 21.34 Acanthamoeba spp. are waterborne parasites very common in unchlorinated aqueous environments. As shown in this life cycle, Acanthamoeba cysts and trophozoites are both capable of entering the body through various routes, causing infections of the eye, skin, and central nervous system. (credit: modification of work by Centers for Disease Control and Prevention)
Figure 21.35 (a) An Acanthamoeba cyst. (b) An Acanthamoeba trophozoite (c) The eye of a patient with Acanthamoeba keratitis. The fluorescent color, which is due to sodium fluorescein application, highlights significant damage to the cornea and vascularization of the surrounding conjunctiva. (credit a: modification of work by Centers for Disease Control and Prevention; credit b, c: modification of work by Jacob Lorenzo-Morales, Naveed A Kahn and Julia Walochnik)


The helminth Loa loa, also known as the African eye worm, is a nematode that can cause loiasis, a disease endemic to West and Central Africa (Figure 21.36). The disease does not occur outside that region except when carried by travelers. There is evidence that individual genetic differences affect susceptibility to developing loiasis after infection by the Loa loa worm. Even in areas in which Loa loa worms are common, the disease is generally found in less than 30% of the population. It has been suggested that travelers who spend time in the region may be somewhat more susceptible to developing symptoms than the native population, and the presentation of infection may differ.

The parasite is spread by deerflies (genus Chrysops), which can ingest the larvae from an infected human via a blood meal (Figure 21.36). When the deerfly bites other humans, it deposits the larvae into their bloodstreams. After about five months in the human body, some larvae develop into adult worms, which can grow to several centimeters in length and live for years in the subcutaneous tissue of the host.

The name “eye worm” alludes to the visible migration of worms across the conjunctiva of the eye. Adult worms live in the subcutaneous tissues and can travel at about 1 cm per hour. They can often be observed when migrating through the eye, and sometimes under the skin; in fact, this is generally how the disease is diagnosed. It is also possible to test for antibodies, but the presence of antibodies does not necessarily indicate a current infection; it only means that the individual was exposed at some time. Some patients are asymptomatic, but in others the migrating worms can cause fever and areas of allergic inflammation known as Calabar swellings. Worms migrating through the conjunctiva can cause temporary eye pain and itching, but generally there is no lasting damage to the eye. Some patients experience a range of other symptoms, such as widespread itching, hives, and joint and muscle pain.

Worms can be surgically removed from the eye or the skin, but this treatment only relieves discomfort; it does not cure the infection, which involves many worms. The preferred treatment is diethylcarbamazine, but this medication produces severe side effects in some individuals, such as brain inflammation and possible death in patients with heavy infections. Albendazole is also sometimes used if diethylcarbamazine is not appropriate or not successful. If left untreated for many years, loiasis can damage the kidneys, heart, and lungs, though these symptoms are rare.

Figure 21.36 This Loa loa worm, measuring about 55 mm long, was extracted from the conjunctiva of a patient with loiasis. The Loa loa has a complex life cycle. Biting deerflies native to the rain forests of Central and West Africa transmit the larvae between humans. (credit a: modification of work by Eballe AO, Epée E, Koki G, Owono D, Mvogo CE, Bella AL; credit b: modification of work by NIAID; credit c: modification of work by Centers for Disease Control and Prevention)

Disease Profile

Parasitic Skin and Eye Infections

The protozoan Acanthamoeba and the helminth Loa loa are two parasites capable of causing infections of the skin and eyes. Figure 21.37 summarizes the characteristics of some common fungal infections of the skin.

Figure 21.37


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SA Bos, M.D.

Lead Author