Introduction to Laboratory Diagnosis of Infectious Disease

Creator: Maria T. Vazquez-Pertejo
Published: 2022-10-06

Maria T. Vazquez-Pertejo

, MD, FACP, Wellington Regional Medical Center

Last review/revision Oct 2022

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Laboratory tests may identify organisms directly (eg, visually, using a microscope, growing the organism in culture) or indirectly (eg, identifying antibodies to the organism). General types of tests include

Culture is normally the gold standard for identification of organisms, but results may not be available for days or weeks, and not all pathogens can be cultured, making alternative tests useful. When a pathogen is cultured and identified, the laboratory can also assess its susceptibility Susceptibility Testing Susceptibility tests determine a microbe’s vulnerability to antimicrobial drugs by exposing a standardized concentration of organism to specific concentrations of antimicrobial drugs. Susceptibility... read more to antimicrobial drugs. Sometimes molecular methods can be used to detect specific resistance genes.

Some tests (eg, Gram stain, routine aerobic culture) can detect a large variety of pathogens and are commonly done for many suspected infectious illnesses. However, because some pathogens are missed on these tests, clinicians must be aware of the limitations of each test for each suspected pathogen. In such cases, clinicians should request tests specific for the suspected pathogen (eg, special stains or culture media) or advise the laboratory of the suspected organism(s) so that it may select more specific tests.

Diagnostic Tests for Some Bacterial Pathogens

Microorganism	Microscopy	Culture	NAAT	Antigen Detection	Antibody Detection
Anaplasma species Ehrlichiosis and Anaplasmosis Ehrlichiosis and anaplasmosis are caused by rickettsial-like bacteria. Ehrlichiosis is caused mainly by Ehrlichia chaffeensis; anaplasmosis is caused by Anaplasma phagocytophilum... read more	✓		✓		✓
Bacillus anthracis Anthrax Anthrax is caused by the gram-positive Bacillus anthracis, which are toxin-producing, encapsulated, facultative anaerobic organisms. Anthrax, an often fatal disease of animals, is transmitted... read more	✓	✓	✓
Bartonella species Overview of Bartonella Infections Bartonella species are gram-negative bacteria previously classified as Rickettsiae. They are facultative intracellular organisms that typically live within red blood cells (RBCs) and... read more	✓		✓		✓
Bordetella pertussis Pertussis Pertussis is a highly communicable disease occurring mostly in children and adolescents and caused by the gram-negative bacterium Bordetella pertussis. Symptoms are initially those of... read more		✓	✓		✓
Borrelia species Lyme Disease Lyme disease is a tick-transmitted infection caused by the spirochete Borrelia species. Early symptoms include an erythema migrans rash, which may be followed weeks to months later by... read more		✓*	✓*		✓
Brucella species Brucellosis Brucellosis is caused by Brucella species, which are gram-negative bacteria. Symptoms begin as an acute febrile illness with few or no localized signs and may progress to a chronic stage... read more	✓	✓	✓		✓
Chlamydia species Chlamydia and Mycoplasmal Mucosal Infections Sexually transmitted urethritis, cervicitis, proctitis, and pharyngitis (that are not due to gonorrhea) are caused predominantly by chlamydiae and less frequently by mycoplasmas. Chlamydiae... read more			✓		✓
Clostridium botulinum Botulism Botulism is poisoning that is due to Clostridium botulinum toxin and that affects the peripheral nerves. Botulism may occur without infection if toxin is ingested, injected, or inhaled... read more	✓	✓		✓
Clostridioides difficile Clostridioides (formerly Clostridium) difficile–Induced Diarrhea Toxins produced by Clostridioides difficile strains in the gastrointestinal tract cause pseudomembranous colitis, typically after antibiotic use. Symptoms are diarrhea, sometimes bloody... read more		✓	✓	✓
Clostridium tetani Tetanus Tetanus is acute poisoning from a neurotoxin produced by Clostridium tetani. Symptoms are intermittent tonic spasms of voluntary muscles. Spasm of the masseters accounts for the name... read more	✓	✓
Corynebacterium diphtheriae Diphtheria Diphtheria is an acute pharyngeal or cutaneous infection caused mainly by toxigenic strains of the gram-positive bacillus Corynebacterium diphtheriae and rarely by other, less common... read more		✓
Coxiella species Q Fever Q fever is an acute or chronic disease caused by the rickettsial-like bacillus Coxiella burnetii. Acute disease causes sudden onset of fever, headache, malaise, and interstitial pneumonitis... read more			✓		✓
Erysipelothrix species Erysipeloid Erysipeloid is infection caused by the gram-positive bacillus Erysipelothrix rhusiopathiae. The most common manifestation is an acute but slowly evolving localized cellulitis. Diagnosis... read more	✓	✓
Francisella tularensis Tularemia Tularemia is a febrile disease caused by the gram-negative bacterium Francisella tularensis; it may resemble typhoid fever. Symptoms are a primary local ulcerative lesion, regional lymphadenopathy... read more		✓			✓
Haemophilus ducreyi Haemophilus Infections The gram-negative bacteria Haemophilus species cause numerous mild and serious infections, including bacteremia, meningitis, pneumonia, sinusitis, otitis media, cellulitis, and epiglottitis... read more	✓	✓
Helicobacter pylori Helicobacter pylori Infection Helicobacter pylori is a common gastric pathogen that causes gastritis, peptic ulcer disease, gastric adenocarcinoma, and low-grade gastric lymphoma. Infection may be asymptomatic or... read more	✓	✓*		✓
Kingella species Kingella Infections Kingella are gram-negative organisms that colonize the human oropharynx. They cause skeletal infections, endocarditis, and bacteremia and, rarely, pneumonia, epiglottitis, meningitis... read more	✓*	✓	✓
Klebsiella species Klebsiella, Enterobacter, and Serratia Infections The gram-negative bacteria Klebsiella, Enterobacter, and Serratia are closely related normal intestinal flora that rarely cause disease in normal hosts. Diagnosis is by... read more	✓		✓
Legionella species Legionella Infections Legionella pneumophila is a gram-negative bacillus that most often causes pneumonia with extrapulmonary features. Diagnosis requires specific growth media, serologic or urine antigen... read more		✓	✓	✓	✓
Leptospira species Leptospirosis Leptospirosis is an infection caused by one of several pathogenic serotypes of the spirochete Leptospira. Symptoms are biphasic. Both phases involve acute febrile episodes; the second... read more		✓*	✓		✓
Listeria species Listeriosis Listeriosis is bacteremia, meningitis, cerebritis, dermatitis, an oculoglandular syndrome, intrauterine and neonatal infections, or rarely endocarditis caused by Listeria species. Symptoms... read more	✓	✓	✓
Mycoplasma species Chlamydia and Mycoplasmal Mucosal Infections Sexually transmitted urethritis, cervicitis, proctitis, and pharyngitis (that are not due to gonorrhea) are caused predominantly by chlamydiae and less frequently by mycoplasmas. Chlamydiae... read more			✓		✓
Neisseria species Meningococcal Diseases Meningococci (Neisseria meningitidis) are gram-negative diplococci that cause meningitis and meningococcemia. Symptoms, usually severe, include headache, nausea, vomiting, photophobia... read more	✓	✓	✓
Nocardia Nocardiosis Nocardiosis is an acute or chronic, often disseminated, suppurative or granulomatous infection caused by various aerobic soil saprophytes of the gram-positive bacilli genus Nocardia.... read more	✓	✓	✓
Rhodococcus equus	✓	✓
Rickettsial species			✓		✓
Streptococcus species Streptococcal Infections Streptococci are gram-positive aerobic organisms that cause many disorders, including pharyngitis, pneumonia, wound and skin infections, sepsis, and endocarditis. Symptoms vary with the organ... read more	✓	✓	✓	✓
Treponema pallidum Syphilis Syphilis is caused by the spirochete Treponema pallidum and is characterized by 3 sequential symptomatic stages separated by periods of asymptomatic latent infection. Common manifestations... read more	✓		✓		✓
Tropheryma whipplei Whipple Disease Whipple disease is a rare systemic illness caused by the bacterium Tropheryma whipplei. Main symptoms are arthritis, weight loss, abdominal pain, and diarrhea. Diagnosis is by small-bowel... read more	✓		✓
Vibrio species Cholera Cholera is an acute infection of the small bowel by the gram-negative bacterium Vibrio cholerae, which secretes a toxin that causes copious watery diarrhea, leading to dehydration, oliguria... read more		✓	✓
Yersinia pestis Plague and Other Yersinia Infections Plague is caused by the gram-negative bacterium Yersinia pestis. Symptoms are either severe pneumonia or large, tender lymphadenopathy with high fever, often progressing to septicemia... read more	✓	✓	✓	✓
Adapted from Bennett JE, Dolin R, Blaser MJ: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 9th Edition. Elsevier, 2020.
* Test not widely available in clinical practice.
NAAT=Nucleic Acid Amplification Test

Diagnostic Tests for Mycobacterial Pathogens

Microorganism	Microscopy	Culture	NAAT	Antibody Detection
Nontuberculous Nontuberculous Mycobacterial Infections There are over 170 recognized species of mycobacteria, mostly environmental. Environmental exposure to many of these organisms is common, but most exposures do not cause infection and many infections... read more	✓	✓	✓*
Tuberculosis Tuberculosis (TB) Tuberculosis is a chronic, progressive mycobacterial infection, often with an asymptomatic latent period following initial infection. Tuberculosis most commonly affects the lungs. Symptoms include... read more and ulcerans	✓	✓	✓
Mycobacterium leprae	✓		✓	✓
Adapted from Bennett JE, Dolin R, Blaser MJ: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 9th Edition. Elsevier, 2020.
* Test not widely available in clinical practice.
NAAT=Nucleic Acid Amplification Test

Diagnostic Tests for Some Fungal Pathogens

Microorganism	Microscopy	Culture	NAAT	Antigen Detection	Antibody Detection
Aspergillus species Aspergillosis Aspergillosis is an opportunistic infection that usually affects the lower respiratory tract and is caused by inhaling spores of the filamentous fungus Aspergillus, commonly present in... read more	✓	✓	✓	✓
Blastomyces species Blastomycosis Blastomycosis is a pulmonary disease caused by inhaling spores of the dimorphic fungus Blastomyces dermatitidis. Occasionally, the fungi spread hematogenously, causing extrapulmonary... read more	✓	✓	✓	✓	✓
Candida species Candidiasis (Invasive) Candidiasis is infection by Candida species (most often C. albicans), manifested by mucocutaneous lesions, fungemia, and sometimes focal infection of multiple sites. Symptoms depend... read more	✓	✓	✓
Coccidioides species Coccidioidomycosis Coccidioidomycosis is a pulmonary or hematogenously spread disseminated disease caused by the fungi Coccidioides immitis and C. posadasii; it usually occurs as an acute benign... read more	✓	✓	✓	✓	✓
Cryptococcus neoformans Cryptococcosis Cryptococcosis is a pulmonary or disseminated infection acquired by inhalation of soil contaminated with the encapsulated yeasts Cryptococcus neoformans or C. gattii. Symptoms... read more	✓	✓	✓	✓
Dermatophytes Overview of Dermatophytoses Dermatophytoses are fungal infections of keratin in the skin and nails (nail infection is called tinea unguium or onychomycosis). Symptoms and signs vary by site of infection. Diagnosis is by... read more	✓	✓
Histoplasma capsulatum Histoplasmosis Histoplasmosis is a pulmonary and hematogenous disease caused by Histoplasma capsulatum; it is often chronic and usually follows an asymptomatic primary infection. Symptoms are those... read more	✓	✓	✓	✓	✓
Malassezia species Seborrheic Dermatitis Seborrheic dermatitis is a common inflammatory condition of skin regions with a high density of sebaceous glands (eg, face, scalp, sternum). The cause is unknown, but species of Malassezia... read more	✓	✓
Mucorales species Mucormycosis Mucormycosis refers to infection caused by diverse fungal organisms in the order Mucorales, including those in the genera Rhizopus, Rhizomucor, and Mucor. Symptoms most... read more	✓	✓	✓
Pneumocystis jirovecii Pneumocystis jirovecii Pneumonia Pneumocystis jirovecii is a common cause of pneumonia in immunosuppressed patients, especially in those infected with human immunodeficiency virus (HIV) and in those receiving systemic... read more	✓		✓	✓
Sporothrix species Sporotrichosis Sporotrichosis is a cutaneous infection caused by the saprophytic mold Sporothrix schenckii. Pulmonary and hematogenous involvement is uncommon. Symptoms are cutaneous nodules that spread... read more	✓	✓			✓
Adapted from Bennett JE, Dolin R, Blaser MJ: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 9th Edition. Elsevier, 2020.
NAAT=Nucleic Acid Amplification Test

Diagnostic Tests for Some Viral Pathogens

Microorganism	Microscopy	Culture	NAAT	Antigen Detection	Antibody Detection
Adenovirus Adenovirus Infections Infection with one of the many adenoviruses may be asymptomatic or result in specific syndromes, including mild respiratory infections, keratoconjunctivitis, gastroenteritis, cystitis, and primary... read more	✓*	✓	✓
BK virus	✓		✓
COVID-19 (SARS-CoV2) COVID-19 COVID-19 is an acute, sometimes severe, respiratory illness caused by the novel coronavirus SARS-CoV-2. Prevention is by vaccination and infection control precautions (eg, face masks, handwashing... read more			✓		✓
Cytomegalovirus (CMV) Cytomegalovirus (CMV) Infection Cytomegalovirus (CMV, human herpesvirus type 5) can cause infections that have a wide range of severity. A syndrome of infectious mononucleosis that lacks severe pharyngitis is common. Severe... read more	✓	✓	✓		✓
Enteroviruses Overview of Enterovirus Infections Enteroviruses, along with rhinoviruses (see Common Cold) and human parechoviruses, are a genus of picornaviruses (pico, or small, RNA viruses). All enteroviruses are antigenically heterogeneous... read more		✓	✓		✓
Epstein-Barr Virus (EBV) Infectious Mononucleosis Infectious mononucleosis is caused by Epstein-Barr virus (EBV, human herpesvirus type 4) and is characterized by fatigue, fever, pharyngitis, and lymphadenopathy. Fatigue may persist weeks or... read more			✓		✓
Hepatitis Overview of Chronic Hepatitis Chronic hepatitis is hepatitis that lasts > 6 months. Common causes include hepatitis B and C viruses, nonalcoholic steatohepatitis (NASH), alcohol-related liver disease, and autoimmune liver... read more A, B, C, D and E			✓	✓	✓
Herpes simplex virus Herpes Simplex Virus (HSV) Infections Herpes simplex viruses (human herpesviruses types 1 and 2) commonly cause recurrent infection affecting the skin, mouth, lips, eyes, and genitals. Common severe infections include encephalitis... read more	✓	✓	✓		✓
Herpes virus 6 Roseola Infantum Roseola infantum is an infection of infants or very young children caused by human herpesvirus 6B (HHV-6B) or, less commonly, HHV-7. The infection causes high fever and a rubelliform eruption... read more			✓		✓
HIV Human Immunodeficiency Virus (HIV) Infection Human immunodeficiency virus (HIV) infection results from 1 of 2 similar retroviruses (HIV-1 and HIV-2) that destroy CD4+ lymphocytes and impair cell-mediated immunity, increasing risk of certain... read more			✓	✓	✓
Human papillomavirus (HPV) Human Papillomavirus (HPV) Infection Human papillomavirus (HPV) infects epithelial cells. Most of the > 100 subtypes infect cutaneous epithelium and cause skin warts; some types infect mucosal epithelium and cause anogenital warts... read more	✓		✓
Influenza Influenza Influenza is a viral respiratory infection causing fever, coryza, cough, headache, and malaise. Mortality is possible during seasonal epidemics, particularly among high-risk patients (eg, those... read more			✓	✓
JC virus Progressive Multifocal Leukoencephalopathy (PML) Progressive multifocal leukoencephalopathy (PML) is caused by reactivation of the JC virus. The disease usually occurs in patients with impaired cell-mediated immunity, particularly patients... read more			✓		✓
LaCrosse virus			✓		✓
Lymphocytic choriomeningitis virus (LCMV) Lymphocytic Choriomeningitis Lymphocytic choriomeningitis is caused by an arenavirus. It usually causes a flu-like illness or aseptic meningitis, sometimes with rash, arthritis, orchitis, parotitis, or encephalitis. Diagnosis... read more			✓		✓
Measles Measles Measles is a highly contagious viral infection that is most common among children. It is characterized by fever, cough, coryza, conjunctivitis, an enanthem (Koplik spots) on the oral mucosa... read more			✓		✓
Monkeypox Monkeypox (Mpox) Monkeypox is caused by the monkeypox virus, an orthopoxvirus structurally related to the smallpox virus. Patients present with a vesicular or pustular rash that may be painful and often... read more	✓		✓
Mumps Mumps Mumps is an acute, contagious, systemic viral disease, usually causing painful enlargement of the salivary glands, most commonly the parotids. Complications may include orchitis, meningoencephalitis... read more			✓		✓
Norovirus Viral gastroenteritis Gastroenteritis is inflammation of the lining of the stomach and small and large intestines. Most cases are infectious, although gastroenteritis may occur after ingestion of drugs and chemical... read more			✓		✓
Parainfluenza Parainfluenza Virus Infections Parainfluenza viruses include several closely related viruses that cause many respiratory illnesses varying from the common cold to an influenza-like syndrome or pneumonia; croup is the most... read more		✓	✓
Parvovirus B19 Erythema Infectiosum Erythema infectiosum, acute infection with parvovirus B19, causes mild constitutional symptoms and a blotchy or maculopapular rash beginning on the cheeks and spreading primarily to exposed... read more			✓		✓
Powassan virus Powassan virus Arbovirus (arthropod-borne virus) applies to any virus that is transmitted to humans and/or other vertebrates by certain species of blood-feeding arthropods, chiefly insects (flies and mosquitoes)... read more			✓		✓
Rabies Rabies Rabies is a viral encephalitis transmitted by the saliva of infected bats and certain other infected mammals. Symptoms include depression and fever, followed by agitation, excessive salivation... read more	✓		✓	✓	✓
Respiratory syncytial virus (RSV) Respiratory Syncytial Virus (RSV) and Human Metapneumovirus Infections Respiratory syncytial virus and human metapneumovirus infections cause seasonal lower respiratory tract disease, particularly in infants and young children. Disease may be asymptomatic, mild... read more		✓	✓	✓
Rubella Rubella ( See also Congenital Rubella.) Rubella is a contagious viral infection that may cause adenopathy, rash, and sometimes constitutional symptoms, which are usually mild and brief. Infection during... read more					✓
St Louis encephalitis virus			✓		✓
Tickborne encephalitis virus					✓
Varicella zoster Chickenpox Chickenpox is an acute, systemic, usually childhood infection caused by the varicella-zoster virus (human herpesvirus type 3). It usually begins with mild constitutional symptoms that are followed... read more	✓	✓	✓		✓
West Nile virus West Nile Virus West Nile virus is a flavivirus that is now the primary cause of arbovirus encephalitis in the US. Most patients have mild or no symptoms. About 1 out of 150 patients develop a severe infection... read more			✓		✓
Zika virus Zika Virus (ZV) Infections The Zika virus is a mosquito-borne flavivirus that is antigenically and structurally similar to the viruses that cause dengue, yellow fever, and West Nile virus. Zika virus infection is typically... read more			✓		✓
Adapted from Bennett JE, Dolin R, Blaser MJ: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 9th Edition. Elsevier, 2020.
* Test not widely available in clinical practice.
NAAT=Nucleic Acid Amplification Test

Diagnostic Tests for Some Protozoal and Parasitic Pathogens

Microorganism	Microscopy	Culture	NAAT	Antigen Detection	Antibody Detection
Babesia Babesiosis Babesiosis is infection with Babesia species of protozoa. Infections can be asymptomatic or cause a malaria-like illness with fever and hemolytic anemia. Disease is most severe in asplenic... read more	✓		✓		✓
Cryptosporidium Cryptosporidiosis Cryptosporidiosis is infection with the protozoan Cryptosporidium. The primary symptom is watery diarrhea, often with other signs of gastrointestinal distress. Illness is typically self-limited... read more	✓		✓	✓
Cyclospora Cyclosporiasis Cyclosporiasis is infection with the protozoan Cyclospora cayetanensis. Symptoms include watery diarrhea with gastrointestinal and systemic symptoms. Diagnosis is by detection of characteristic... read more	✓		✓
Entamoeba Amebiasis Amebiasis is infection with Entamoeba histolytica. It is acquired by fecal-oral transmission. Infection is commonly asymptomatic, but symptoms ranging from mild diarrhea to severe dysentery... read more	✓		✓	✓	✓
Enterobius vermicularis Pinworm Infestation Enterobiasis is an intestinal infestation by the pinworm Enterobius vermicularis, usually in children, but adult members of their household and caregivers, institutionalized people, and... read more	✓
Giardia Giardiasis Giardiasis is infection with the flagellated protozoan Giardia duodenalis (G. lamblia, G. intestinalis). Infection can be asymptomatic or cause symptoms ranging from intermittent... read more	✓		✓	✓
Intestinal nematodes	✓			✓	✓
Leishmania species Leishmaniasis Leishmaniasis is caused by species of Leishmania. Manifestations include cutaneous, mucosal, and visceral syndromes. Cutaneous leishmaniasis causes painless chronic skin lesions ranging... read more	✓	✓	✓		✓
Plasmodium species Malaria Malaria is infection with Plasmodium species. Symptoms and signs include fever (which may be periodic), chills, rigors, sweating, diarrhea, abdominal pain, respiratory distress, confusion... read more	✓		✓	✓
Scabies Scabies Scabies is an infestation of the skin with the mite Sarcoptes scabiei. Scabies causes intensely pruritic lesions with erythematous papules and burrows in web spaces, wrists, waistline... read more	✓
Taenia solium Taenia Solium (Pork Tapeworm) Infection and Cysticercosis Taenia solium infection (taeniasis) is an intestinal infection with adult tapeworms that follows ingestion of contaminated pork. Adult worms may cause mild gastrointestinal symptoms or passage... read more	✓				✓
Toxocara species Toxocariasis Toxocariasis is human infection with nematode ascarid larvae that ordinarily infect animals. Symptoms are fever, anorexia, hepatosplenomegaly, rash, pneumonitis, asthma, or visual impairment... read more	✓				✓
Trichinella spiralis Trichinosis Trichinosis is infection with Trichinella spiralis or related Trichinella species. Symptoms include initial gastrointestinal irritation followed by periorbital edema, muscle pain... read more	✓				✓
Trypanosoma species African Trypanosomiasis Human African trypanosomiasis is infection with protozoa of the species Trypanosoma brucei, transmitted by the bite of a tsetse fly. Symptoms include characteristic skin lesions, intermittent... read more	✓				✓
Adapted from Bennett JE, Dolin R, Blaser MJ: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 9th Edition. Elsevier, 2020.
NAAT=Nucleic Acid Amplification Test

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