Chapter 40
Microbiologic Diagnosis of Ocular Infections
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Establishing the etiology of ocular infections requires collecting appropriate specimens and performing definitive laboratory studies.1,2 Some physicians process and examine clinical specimens in their offices,3 but most ophthalmologists use a microbiology laboratory. The microbiologist efficiently handles small samples and differentiates microorganisms commonly associated with healthy and infected eyes.
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Material is collected for smears, cultures, and other diagnostic tests when available. Scrapings and swabbings are used to obtain material from the ocular surface. Intraocular fluids are obtained by syringe aspiration or vitrectomy instrumentation.4 Material is put into a transport container or inoculated directly onto enriched microbiologic media. A tissue biopsy is aseptically placed in a transport medium or preservative-free saline for homogenization.5,6 Foreign bodies, ophthalmic solutions, contact lenses, and other biomaterials can also be sent for microbiologic analysis.

Clinical samples are labeled with the patient's name, type of tissue or fluid, and the date of collection. Universal precautions are followed during collection and processing. Specimens that are shipped elsewhere are put inside double mailing containers with a biohazard label and sent according to current postal regulations.

Submitting specimens and a requisition form to the microbiology laboratory starts a sequence of procedures designed to identify infecting microorganisms (Fig. 1). In the laboratory, smears are stained and examined, other rapid diagnostic tests are performed if possible, and inoculated culture media or cell lines are incubated under specific temperature and environmental conditions to enhance growth.

Fig. 1. Steps in the laboratory evaluation of ocular infection.

The laboratory is staffed by accredited personnel who maintain a quality-assurance program with a procedure manual that includes periodic monitoring of equipment and supplies. Communication networks are maintained between office and laboratory personnel to facilitate timely distribution of laboratory test results. Suspected false-negative tests may indicate a need to contact the clinician for additional specimens.7 Results are also reported, when indicated, to the appropriate public health agency.

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Microscopic examination of ocular specimens is a common diagnostic test for confirming ocular infections. The instrument that collects the material must be clean and sterile to avoid particles that could cause staining artifacts.

Smearing the specimen in a thin film on a clean glass slide evenly distributes microorganisms. Thick smears cause some stains to clump, whereas excessive spreading fragments cells. Etched circles on the slide or rings made with a wax pencil help the microscopist to find the inoculation site. The examiner must be familiar with the various instruments and methods of microscopy.8


Scrapings and swabbings of the ocular surface and samples of intraocular fluids can be examined directly by brightfield illumination. Background light is reduced by reducing the microscope's iris diaphragm. Microscopy of fresh, unstained specimens can delineate cells, but differentiation is difficult.

A saline mount is infrequently used in ocular microbiology but can demonstrate large parasites such as mites (Demodex) and lice (Phthirus pubis) from the eyelashes. Onchocercal microfilariae can be directly observed wriggling out of a scraping or biopsy submerged in saline or Hawk's solution.9,10

Phase-contrast microscopy and Nomarski optics demonstrate the motility of viable organisms (e.g., Acanthamoeba trophozoites).11 Darkfield microscopy increases the visibility of translucent microbes such as spirochetes12 and spores.

Potassium hydroxide (KOH) 10% is sometimes mixed with the specimen to digest keratinized epithelial cells or thick mucin strands that might be confused with fungal elements. The KOH wet mount can be useful for detecting fungi from ocular specimens.13,14

Opaque suspensions of India ink or nigrosin help to outline formed elements such as fungi.15 Lactophenol cotton blue can be used in a wet mount of a clinical specimen to reveal fungi16 and amebic cysts.17 This stain is also used to examine yeasts and the spores of filamentous fungi grown on cultures.


A specimen is fixed to a glass slide so staining solutions do not wash it off. Heat fixation by passing the slide through a hot flame is satisfactory, but cytologic details are better preserved by alcohol fixation. The slide is flooded or immersed in a Coplin jar of methanol for 3 to 5 minutes. Methanol is also useful to prepare specimens for immunofluorescent processing.

Staining makes many microorganisms easier to see and helps to classify microbes and human cells.18 Examination of stained smears begins with scanning the slide under low power. The microscopist looks for inflammatory cells, epithelial cells, other tissue cells, and mucus with an eye to recognize the cytopathologic pattern.18 Without seeing at least 10 cells in a low-power field, the laboratory will probably question whether sufficient material was obtained. Stained smears are efficient in the evaluation of bacterial and fungal infections19 and are often the easiest way to confirm parasitic disease.20

Several staining methods are available to evaluate ocular specimens (Table 1). Basic dyes (e.g., hematoxylin) stain acidic structures such as nuclear chromatin. Acidic dyes (e.g., eosin) stain basic substances in the cytoplasm. Stains capable of fluorescence glow under ultraviolet light and make it easier to find microorganisms scattered on a smear. Extra, unstained smears are frozen to prevent breakdown of microbial and viral components. Several stains have high predictive value (Table 2) for confirming chlamydial conjunctivitis,21–24 bacterial keratitis,25–27 fungal keratitis,14,26–30 or endophthalmitis.31

TABLE 1. Microscopic Procedures Used in Ocular Microbiology

Acid-fast stain1. Flood fixed smear with carbolfuchsin solution for 2 minutes.
2. Rinse with water, then decolorize with 3% acid-alcohol.
3. Rinse with water, then flood with methylene blue counterstain for 20 minutes.
4. Rinse and air dry.
Acridine orange stain1. Flood slide with acidic (pH 4) acridine orange solution.
2. Wait 2 minutes.
3. Rinse with water and dry.
4. Examine under oil immersion with ultraviolet light.
Calcofluor white stain1. Add 1 drop of 0.1% calcofluor white/0.1% Evans blue solution to specimen on a glass slide.
2. Apply coverslip.
3. Examine with ultraviolet light.
Darkfield examination1. Mix specimen in saline.
2. Apply coverslip.
3. Examine with darkfield condenser.
Giemsa stain1. Add freshly prepared Giemsa solution to fixed smear for 45-60 minutes.
2. Rinse in 95% ethanol.
Gram's stain1. Flood fixed smear with crystal violet solution for 1 minute.
2. Rinse with water, then flood with Gram's iodine solution for 1 minute.
3. Rinse with water, then decolorize with drops of acetone-alcohol solution.
4. Rinse with water, then flood with safranin counterstain for 30 seconds.
5. Rinse with water and blot dry.
Germ test tube1. Mix yeast in serum.
2. Incubate at 35° to 37°C for up to 3 hours.
3. Examine under low power for germ tubes extending from yeasts.
India ink mount1. Mix specimen with one drop of India ink or nigrosin.
2. Apply coverslip.
Lactophenol cotton blue1. Mix specimens with one drop of lactophenol cotton blue stain.
2. Apply coverslip.
Methenamine-silver stain1. Flood fixed smear with chromic acid solution.
2. Rinse with water, then flood with 1% sodium bisulfate for 1 minutes.
3. Rinse with water, then flood with fresh methenamine-silver nitrate solution and heat.
4. Rinse with water, then flood with 0.1% gold chloride for 2 minutes.
5. Rinse with water, then flood with 2% sodium thiosulfate solution for 2 minutes.
6. Rinse with water, then flood with fresh, light green counterstain for 1 minute.
7. Rinse and dry.
Periodic acid-Schiff stain1. Immerse fixed smear in 95% ethanol for 1 minute.
2. Immerse in 5% periodic acid for 1 minute.
3. Immerse in basic fuchsin solution for 2 minutes.
4. Rinse with water then immerse in picric acid counterstain for 2 minutes (light green for 5 seconds).
5. Rinse with water and dry.
6. Dehydrate in 95% ethanol for 10 seconds, followed by absolute ethanol for 1 minute.
7. Clear in xylene.
Wet mount1. Mix specimen in 0.85% saline or 10% potassium hydroxide (KOH).
2. Apply coverslip.
3. Put paraffin-petrolatum around edges to reduce drying.
Trichrome stain1. Use cytology fixative and immerse slide in 70% ethanol for 5 minutes.
2. Immerse in alcohol-iodine solution for 3 minutes.
3. Immerse twice in 70% ethanol for 5 minutes.
4. Immerse in trichrome (chromotropic/light green/phosphotungstic acid) for 5 minutes.
5. Decolorize with acid-alcohol.
6. Rinse with ethanol.
Warthin-Starry stain1. Immerse slide in warm 1% silver nitrate solution for 30 minutes.
2. Flood with warm developer solution until light brown.
3. Rinse with hot water and dehydrate.
4. Clear in xylene.


TABLE 2. Performance of Microscopic ExaminationCompared to Culture for Ocular Infections

DiseaseSpecimenTestSensitivitySpecificityPositive Predictive Value
Chlamydial conjunctivitisConjunctivaGiesma stain8%–43%82%–100%74%–100%
Bacterial keratitisCorneal scrapingGram's stain36%–65%65%–92%61%–84%
Acridine orange81%89%88%
Fungal keratitisCorneal scrapingGram's stain54%–98%83%94%– 00%
Acridine orange76%92%80%
KOH wet mount33%–99%89%–99%73%–98%
Calcofluor white61%–95%84%80%
Methenamine silver86%–89%
Lactophenol cotton blue78%95%88%
EndophthalmitisAqueous humorGram's stain43%95%97%
Vitreous humorGram's stain17%97%97%

KOH, potassium hydrochloride.



Gram's Stain

Gram's staining is a standard method in bacteriology laboratories. Crystal violet is applied, then bound to bacterial cells by a weak iodine solution. An acetone-alcohol solvent removes the dye from bacteria whose cell walls lack teichoic acid cross-links that resist decolorization. Dye-retaining, gram-positive bacteria remain dark blue, while gram-negative bacteria are counterstained pink-red with safranin. Color and shape help in presumptive classification. Modifications such as the Brown-Hopps stain are applicable to tissue sections. A fluorescent modification is not as sensitive as the conventional Gram's stain.32

In microbial keratitis, Gram's staining successfully identifies the responsible organism in many culture-positive cases.33 During endophthalmitis, the Gram's stain is also useful, although less sensitive, in evaluating vitreous aspirates.34 Gram's staining has some utility for diagnosing bacterial conjunctivitis35–37 but has high predictive value for gonococcal and meningococcal conjunctivitis. Caution is needed to avoid overinterpreting the Gram's-stained smear. Presumptive identification must be verified by culture isolation.

Giemsa Stain

Methylene blue stains nucleic acids in microorganisms, leukocytes, and tissue cells blue against a light gray background. Giemsa's methylene blue derivative enhances visualization. Modified Giemsa staining highlights DNA in human cell nuclei and cytoplasmic RNA in lymphocytes. Bacteria, intracellular chlamydial elementary bodies, and many viral inclusions stain dark blue. Fungi and parasites are visualized by precipitation of the stain upon their outer walls.

Giemsa staining is used selectively in microbiology laboratories.21,38–40

Indications are to screen smears for small gram-negative bacteria, such as Haemophilus and Neisseria, that might be missed by Gram's staining; to evaluate inflammatory cells in ocular specimens21,37,41,42; to detect protozoa such as acanthamoebic cysts, microsporidial spores, and leishmanid amastigotes; and to reveal intracytoplasmic inclusions during chlamydial conjunctivitis.40

Giemsa staining is useful for evaluating the cytologic pattern21,38 and cellular details39 of conjunctival specimens (Table 3). Other Romanowsky stains are Wright's stain, used to evaluate conjunctival cytology, and Field's stain, used to detect protozoa.43 The Tzanck smear of fluid from a herpetic vesicle can be stained with Giemsa or Papanicolaou stain to show multinucleated cells.

TABLE 3. Ocular Cytologic Examination

Normal epithelial cellsHomogeneous, light-staining cytoplasm with darkly staining, central, round nucleus. Cells tend to clump together in sheets.
Degenerated epithelial cellsFaint, ghostlike appearance with faded nucleus.
Keratinized epithelial cellsEosinophilic cytoplasmic granularity. The nucleus ultimately degenerates and the cytoplasm becomes darker. Bacteria may adhere to keratin on cell surface.
Goblet cellsIntracellular clump of pale-staining mucus displaces cytoplasm and nucleus.
NeutrophilsPolymorphonuclear granulocyte with fairly homogenous cytoplasm containing pale or nonstaining granules. Dark granules sometimes occur during toxic or infectious inflammation.
EosinophilsPolymorphonuclear granulocyte with bilobed nucleus. Uniformly spherical granules fill cytoplasm. Ruptured cells produce extracellular granules and Charcot-Leyden crystals.
Basophils and mast cellsPolymorphonuclear granulocyte with banded or lobulated nucleus. Dark, basophilic granules of various sizes are unevenly distributed in cytoplasm.
LymphocytesLarge nucleus with scant, faintly staining cytoplasm containing a few scattered eosinophilic granules or vacuoles.
Monocytes and macrophagesLarge, indented or convoluted nucleus within gray-blue cytoplasm. Pseudopods or irregular cytoplasmic margins. Large macrophages engorged with phagocytized particles called histiocytes, epithelioid cells, or Leber cells.
Plasma cellsVelvety cytoplasm that is paler adjacent to an eccentric nucleus.
ErythrocytesDonut-shaped red blood cells without a nucleus
Multinucleated cellsSyncytium of coalescent epithelial cells
Giant cellsMultinucleated macrophages
Pigment granulesBrown granules from the uvea (spheres) and retinal pigment epithelium (ellipsoids)
Mucus and proteinBasophilic mucin and eosinophilic fibrin strands have various threadlike shapes. Collagen fibers tend to be linear.
Cytoplasmic inclusionsBasophilic, intracytoplasmic inclusions capping the nucleus, sometimes called Halberstaedter-vonProwazek inclusions, caused by accumulated elementary bodies of Chlamydia trachomatis. Extracellular elementary bodies are too small to be detected by light microscopy alone.
Nuclear inclusionsEosinophilic, intranuclear inclusions surrounded by a pale halo, sometimes called Lipschütz bodies. Cowdry type A bodies typify herpesvirus infections. Nuclear chromatin is usually clumped along the nuclear margin, and nucleolus is displaced.
Tumor cellsVariable cell size and shape with aberrant nuclei. Many mitotic figures.


Acid-Fast Stains

Lipids and waxes of the mycobacterial cell wall resist staining, but once overcome they then prevent decolorization by acid-alcohol solvents. After applying heat (Ziehl-Neelsen technique) or detergents (Kinyoun method), carbolfuchsin binds to long-chain fatty acids in the cell wall. Mycobacteria stain red against a blue-green background.44 Other organisms detectable with acid-fast staining are microsporidial spores. A modification helps to visualize Nocardia.

Hematoxylin and Eosin Staining

Hematoxylin and eosin are routinely used to stain tissue sections. Bacteria, fungi, acanthamoebæ,45,46 and microsporidia stain satisfactorily. This method is most useful for evaluation of inflammatory and tissue cells.

Trichrome Staining

The trichrome stain is useful to detect protozoa such as acanthamoebæ and microsporidia.47

Periodic Acid-Schiff Staining

The periodic acid-Schiff (PAS) reaction stains certain carbohydrates. PAS can reveal fungi and amoebæ in tissue sections of ocular infections. PAS staining has been used for cytologic diagnosis of uveitis during Whipple's disease.48

Silver Stains

Methenamine-silver nitrate staining is sometimes used in suspected fungal infections. Black fungal cell walls are highlighted against a transparent green background.49 Other silver stains are available to detect spirochetes, microsporidia, and protobacteria. The Dieterle stain helps to demonstrate Borrelia burgdorferi during Lyme disease and Treponema pallidum during early syphilis. The Warthin-Starry silver impregnation method is used to identify the organisms of cat-scratch disease in a conjunctival biopsy.50

Enzyme-Conjugated Stains

Enzymes, such as horseradish peroxidase and alkaline phosphatase, linked to specific antibodies can catalyze a chromogenic reaction to reveal microbial and viral antigens. Horseradish peroxidase results in an orange-brown precipitate. Immunoperoxidase staining has been used for evaluating epithelial keratitis caused by herpes simplex virus51,52 or Epstein-Barr virus.53


Acridine Orange

Acridine orange is a useful screening stain because bacteria stain brightly against a dark background and can be detected at relatively low concentration. Cytopathologists use acridine orange at neutral pH to distinguish greenish viable cells from dead cell nuclei that are red-orange. Microbiologists use this chemofluorescent dye at acidic pH to stain bacteria orange against a dark green background containing polymorphonuclear leukocytes with orange nuclei. Nonviable bacteria stain light yellow-green. Atypical mycobacteria are a faint yellow-orange. Yeasts and amebic cysts stain orange. Filamentous fungi and amebic trophozoites remain green.

A fluorescent microscope or a microscope with an ultraviolet light filter is used to examine acridine orange-stained smears. Staining intensity gradually fades, so smears should be examined within 2 hours. Staining artifacts include faint yellow-orange granules from disintegrating leukocytes.

Acridine orange is a useful stain to screen specimens from bacterial,25,54 fungal,28 and acanthamoebic55 ocular infections (Fig 2). Once microorganisms are identified, a Gram's stain can be performed on the same slide.

Fig. 2. Corneal scrapings stained with acridine orange show chemofluorescent cocci against a dark background with many polymorphonuclear leukocytes from a case of Streptococcus pneumoniae keratitis.

Calcofluor White

Calcofluor white is a colorless dye used as a fabric brightener because it binds to carbohydrate polymers and reflects short-wavelength visible light. This fluorochrome combines with polysaccharides such as chitin that are present in fungal cell walls and in the exocyst of Acanthamoeba. Evans blue is used as a counterstain to stain cells and tissue debris dark red. Under ultraviolet light, calcofluor white stains yeasts, psuedohyphae, hyphae, and amoebic cysts bright apple-green against a dark background.56–58 Smears can be subsequently Gram's or silver-stained.


Fluorochrome dyes such as rhodamine and auramine bind directly to mycolic acid in the mycobacterial cell wall and can be detected by fluorescent microscopy. With potassium permanganate as a counterstain, mycobacteria, Nocardia, and microsporidial spores stain yellow against a dark green background when viewed with a fluorescein isothiocyanate light filter. Mycobacteria are usually easier to detect with a fluorochrome stain than with acid-fast staining, but not all atypical mycobacteria stain equally well with rhodamine-auramine. A carbolfuchsin acid-fast stain can be done on the same slide.

Fluorescein-Conjugated Stains

Fluorescein isothiocyanate (FITC) can be bound to proteins known to target particular microbial components, such as antibodies and lectins. Fluorescein-conjugated monoclonal antibodies are available to detect several microorganisms and viruses. Lectins are glycoproteins, such as wheat-germ agglutinin and concanavalin A, that bind to microbial cell-wall polysaccharides.59 Optimal use of fluoresceinated lectins is limited by the changing carbohydrate composition of microbial cell walls during different growth phases and under different environmental conditions.

Fluorescent microscopy requires appropriate exciter and barrier filters. Immersion oils, if used, should be low-fluorescing. A high-quality laboratory microscope can be retrofitted with epi-illumination using halogen lamps and interference filters to perform fluorescent microscopy.


The limit of light microscopy is approximately 200 nm. Except for vaccinia and other poxviruses, with diameters of approximately 250 nm, individual viruses cannot be seen with direct microscopic observation using visible light.

Transmission electron microscopy is not generally used for rapid diagnosis except for organisms that cannot be identified by other means. The specimen may be fixed, but better resolution occurs if the fresh specimen is processed immediately. Specific antibody is added for immunoelectron microscopy. Electron-dense substances such as phosphotungstic acid and uranyl acetate negatively stain viruses against a darkly contrasting background.

Presumptive viral identification is based upon the presence or absence of an envelope and the shape and arrangement of the nucleocapsid.60,61 Transmission electron microscopy is also helpful in the taxonomy of other microorganisms. For example, the spirals of the polar filament of microsporidia aid in classification.

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Amebocytes are cells circulating in the hemolymph of the horseshoe crab (Limulus polyphemus) that coagulate when exposed to gram-negative bacteria. Standardized lysates of Limulus amebocytes can detect endotoxin. The clinical specimen is mixed in pyrogen-free water, and test reagents are added. Bacterial endotoxin, if present, activates a proclotting enzyme. This reaction is detected by clot formation, turbidity, or a color reaction that gives a yellow solution.

The Limulus lysate test is very sensitive but is specific only for gram-negative bacteria. A positive test indicates the presence and amount of endotoxin but does not assess the viability of organisms in the sample. The assay is applicable to the diagnosis of bacterial keratitis62 and to the detection of gram-negative bacterial contaminants in contact lens paraphernalia.63


Bacteria and other microorganism produce enzymes. Chromogenic and fluorogenic substrates can detect these enzymes, which permits rapid identification of many bacterial and yeast culture isolates. Automated instrumentation is under development that could apply these laboratory methods of bacterial classification to clinical specimens.


Gas-liquid chromatography is commonly applied to the identification of anaerobic bacteria by assessing the production of fatty acids in broth culture. This technique can potentially be used to detect microbial cell-wall components of microorganisms in clinical specimens. Among the constituents that could help in preliminary identification are short- and long-chain fatty acids, aliphatic and aromatic amines, isoprenoid quinones, and certain carbohydrates.

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Primary culture media are selected for the suspected infectious agent (Table 4). Specimens should be obtained from the infected tissue or compartment.64 One or more culture media are directly inoculated.65 Solid media are inoculated directly. Material is transferred to a moistened calcium alginate swab to inoculate liquid media.66 Large volumes of fluids (e.g., from a vitrectomy) can be inoculated into blood culture bottles, concentrated by centrifugation, or vacuum-filtered. Certain collection techniques permit semiquantitative evaluation of subsequent microbial growth. A transport medium can be used if direct inoculation onto primary culture media is not feasible.67

TABLE 4. Media Commonly Used for IsolatingMicroorganisms from Ocular Specimens

Blood agar Many aerobic bacteria, actinomycetes, and fungi. Can be incubated anaerobically.
Brain-heart infusionGentamicin (5 μg/mL)Fungi
Brucella agar* Anaerobes
Chlamydial transport medium (SPG)Gentamicin (50 μg/mL)Vancomycin (100 μg/mL)Nystatin (25 μg/mL)Chlamydia specimen collection
Chocolate agar Many aerobic organisms, including Neisseria, Moraxella, and Haemophilus species
Chopped meat infusion Anaerobes
Lőwenstein-Jensen‡Malachite green 2%Atypical mycobacteria
Nonnutrient agar with bacterial overlay Acanthamoeba
Page amoeba saline Acanthamoeba specimen collection
Sabouraud's dextrose agarGentamicin (20 μg/mL) Chloramphenicol (50 μg/mL)Fungi
Thioglycolate broth Anaerobes and microaerophilic bacteria
Trypticase soy broth Specimen collection
Viral transport mediumPenicillin (100,000 U/mL) Gentamicin (50 μg/mL) Amphotericin B (250 μg/mL)Viral specimen collection

* Schaedler agar also available for recovery of anaerobes.
† Thayer-Martin agar also available, which contains antibiotics to inhibit bacteria and fungi other than Neisseria.
‡ Middlebrook and Petragnani agars are also available for isolation of mycobacteria.



Inoculated media are incubated at appropriate temperatures: 35°C to 37°C for most bacterial cultures, 25°C for fungal cultures, and 30°C to 35°C for amebic cultures. Dehydration is prevented by sealing the plate, using a plastic bag, or placing the plate in a jar to keep humidity at 70% or greater. Many bacteria grow well in an atmosphere of 5% to 10% carbon dioxide (e.g., candle jar or sealed bag with a CO2 generator).

Early growth is detected on inoculation marks with a dissecting microscope or magnifying lens. Delayed recovery is more likely among patients receiving prior antibiotic therapy.68 The characteristics and number of each colony type are noted. Colonies are described according to form, elevation, margination, color, surface, density, consistency, odor, hemolysis, and pigmentation production (Table 5). Representative colonies are picked for staining, biochemical testing (Table 6), and subculture.

TABLE 5. Colony Types of Common Ocular Isolates

Colony MorphologyExamples of Common Organisms
Creamy, convex, smooth-edged colony with β-hemolysisStaphylococcus
Translucent, pinpoint, convex or pulvinate colony with β-hemolysisStreptococcus
Translucent, mucoid, flat or umbilicate colony with α-hemolysisStreptococcus pneumoniae
Gray-green, opaque, flat colony with erose or spreading margins; fruity odorPseudomonas
Semiopaque, gray, pulvinate colony with variable hemolysisEnterobacteriaceae
Gray, flat colony spreading over agarProteus
Creamy, smooth colonyCandida
White, gray, or pigmented colony with fluffy margins and surfaceFilamentous fungus


TABLE 6. Some Common Biochemical Tests Used in the Initial Identification of Bacteria

Bile solubilityIdentify Streptococcus pneumoniae
CatalaseDifferentiate staphylococci (positive) from streptococci (negative)*
CoagulaseIdentify Staphylococcus species
IndoleIdentify gram-negative enteric rods
OxidaseDifferentiate Enterobacteriaceae (negative) from other gram-negative rods

*Erythrocytes contain catalase and can produce a false-positive reaction.


Bacterial species identification is based on detecting unique enzymes by chemical indicators and other tests.69 Fungi are identified by their macroscopic and microscopic morphology.70,71 Clonal identity of isolates from two sources can be compared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and plasmid DNA analysis.72


Viral and chlamydial specimens are sent to the laboratory for inoculation and incubation as soon as possible. If delay is unavoidable, specimens are refrigerated, but not frozen, in a standard refrigerator. A cell line appropriate to the suspected pathogen is selected.

Most virology laboratories use a diploid cell line, such as human fibroblasts (e.g., MRC-5) or human embryonic kidney, or a heteroploid cell line, such as McCoy (unknown origin), Vero (African green monkey kidney), HeLa (human cervical carcinoma), or HEp-2 (human laryngeal carcinoma). The ophthalmologist should tell the laboratory which virus is suspected because most viruses can be isolated on certain cell lines but not others.

Viral specimens are inoculated onto a cell monolayer and incubated at 37°C. Any residual material can be retained at −70°C. For enhanced isolation, the specimen may be centrifuged onto a cell monolayer in a shell vial or microplate. The centrifugation-shell vial system can culture virus and intracellular bacteria.

Cell cultures are periodically examined with light microscopy for any viral cytopathic effect (CPE). The pattern of CPE helps with provisional identification. Complete identification of viral isolates usually involves immunofluorescence or enzyme immunoassay. Chlamydial inclusion bodies are detected in vitro by iodine staining or direct neutralization and hemagglutination assays. Negative cultures can be repassaged.

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Antimicrobial sensitivity testing identifies the minimal inhibitory concentration (MIC) for selected drugs. The drug that is being clinically selected is ideally tested in vitro, but in practice a representative from a related antibiotic class is usually chosen. Panels for gram-positive and gram-negative bacteria are available commercially. The availability of antifungal and antiamebic susceptibility testing is limited.

Relationships between achievable ocular drug levels and sensitivity concentrations vary for different types of ocular infections and various routes of drug delivery. Thus, the terms resistant and sensitive for ocular isolates may lack accurate clinical correlation for many eye infections.


In the Kirby-Bauer method, the microbial inoculum is cultured on Mueller-Hinton agar, and antibiotic-impregnated discs are applied. After incubation, the diameter of the zone of inhibition around each disc gives an approximation of susceptibility (except that oxacillin resistance implies resistance to other β-lactams regardless of other disc readings). Slow-growing bacteria and anaerobes cannot be adequately tested with a disc-diffusion method.


Each antibiotic is serially diluted in sequential tubes or in wells of a microtiter plate. The MIC is recorded as the lowest concentration with no visible growth. The wells with inhibited growth can be subcultured to determine the minimal lethal (bactericidal or fungicidal) concentration. Checkerboard sensitivity testing determines the combined effect of two antimicrobial agents.73


An antimicrobial agent can be incorporated into agar plates at a given concentration. Multiple plates are needed to determine the MIC. This method is reserved for testing some anaerobic bacteria.

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