Chapter 18
GENERAL PRINCIPLES of MICROBIOLOGY and INFECTIOUS DISEASE

Woodhall Stopford*

Common occupational and environmental biological hazards include microorganisms (viruses, rickettsia, chlamydiae, bacteria, fungi, and parasites), allergens of biological origin (e.g., the aeroallergenic fungi and animal dander), and the by-products of microbial growth (e.g., the endotoxins and mycotoxins). Because of their invisible and frequently undetectable nature, biohazards are considered “silent hazards.” Among the occupations associated with biohazards are the healthcare industry, agriculture, science and technology, livestock management, fish and shellfish processing, forestry, waste management, and recreation management.

Microorganisms are found everywhere in nature. They inhabit all environmental niches from the polar icecap to the tropics and deserts. Microorganisms are intimately associated with all living species. Many forms are present as the normal flora of the skin and body orifices, whereas others may cause disease. Most of the microorganisms found on earth, including most of the human and animal pathogens, belong to the mesophilic species, which survive best at ambient temperatures of 20–400°C. Microorganisms that require elevated temperatures for growth belong to the thermophilic species and those that thrive at lower temperatures belong to the psychrophilic species.

The human host is constantly exposed by a variety of routes to biological materials, including living microbes and their products. Humans are also the source of many microorganisms through the shedding process, whereby thousands of organisms are released continuously from the skin, mucous membranes, and body orifices. The great majority of these microorganisms are harmless to us and to our ecosystem. Most are saprophytic organisms that live on inanimate substrates and represent normal human and environmental flora. Nevertheless, pathogenic microorganisms have had a tremendous impact on humankind throughout history, with devastating pandemics of smallpox, yellow fever, influenza, AIDS, plague, tuberculosis, and malaria.

There is also a potential for new infectious diseases of occupational significance to emerge, such as hantaviruses and coronoaviruses. Such outbreaks could result from environmental changes, microbial adaptation, or population movements. Awareness of workplace biohazards is critical to the prevention of occupational disease; complacency can result in serious and life-threatening illness.

Microorganisms found in the workplace range from extremely small viruses and single-celled bacteria to multicellular fungi and parasites. To understand how these organisms produce disease, it is necessary to know how they function, how disease is transmitted, and what factors influence whether infection will develop.

ETIOLOGY OF DISEASE

When Robert Koch discovered the causative microbe of anthrax in 1876, he formulated criteria to establish that a specific microorganism was the cause of a clinically discernible disease. These criteria, known as Koch’s postulates, stipulate that:

  1. The specific organism must be found in diseased animals and not in healthy animals.
  2. The specific organisms must be isolated from the diseased animal and grown in pure culture.
  3. The identical disease must be produced upon inoculation of healthy susceptible animals with a pure culture of the originally isolated organism.
  4. The identical organism must be isolated from the experimentally infected animal.

Microorganisms that can produce disease are classified into categories including viruses, rickettsia, coxiella, ehrlichia, anaplasma, chlamydia, bacteria, fungi, and parasites.

Viruses

Viruses represent the smallest etiologic agent of human diseases (measuring 20–300 nm). They are responsible for the great majority of human infections, especially through inhalation. The classification of viruses depends on the following criteria: (i) morphology, (ii) the presence of envelopes surrounding the viral capsid, (iii) the type of genetic material (RNA or DNA), (iv) organs and tissues preferentially infected, and (v) the nature of disease caused. All viruses are obligate intracellular parasites. Viruses cannot multiply outside the host cell. Their survival as naked particles in the environment is limited, ranging from several hours to a few weeks. Viruses can only infect cells where appropriate receptors are present. When a virus infects a host cell, it utilizes the metabolic machinery of that cell to replicate itself.

Viruses may contain either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) as their genetic material. If the virus contains DNA, this nucleic acid is a recognizable substrate for the host cell’s DNA polymerase enzymes. These enzymes translate the DNA into messenger RNA (mRNA). The mRNA is then transcribed by the host cell’s ribosomes into viral proteins. By contrast, the RNA in RNA viruses is not recognized by the host cell’s ribosomes. These viruses, classified as retroviruses, contain a unique enzyme known as reverse transcriptase. This enzyme allows for transcription of infecting viral RNA to host cell DNA within infected cells. Once this DNA is created, the genetically programmed viral replication proceeds in a manner similar to that for DNA viruses. The replication process results in the production of many additional copies of the infecting virus. These are subsequently liberated into the surrounding milieu to infect other target cells. Some viruses, termed cytopathogenic viruses, cause the destruction of the host cell during the replication process.

Rickettsia, Coxiella, Ehrlichia, and Anaplasma

The Rickettsia, Coxiella, Ehrlichia, and Anaplasma are primarily intracellular parasites, although they are considerably more complex than the viruses. They are coccobacillary in morphology, contain both RNA and DNA, and resemble the Gram-negative bacteria. As intracellular parasites, the rickettsiae multiply through the process of binary fission. They are completely independent of host cell metabolic activity. Most rickettsial agents are transmitted to humans through arthropod vectors, for example, the transmission of Rocky Mountain spotted fever by the Dermacentor tick. However, Q fever, caused by Coxiella burnetii, is readily transmitted through contaminated aerosols and has been responsible for numerous laboratory-acquired infections. Outdoor sites represent the greatest risk of rickettsial infection for workers, including those employed in agriculture, forestry, and construction.

Chlamydiae

Chlamydiae are usually classified as belonging to the domain of the bacteria, although many authors separate them for purposes of discussion. Like viruses, chlamydiae are obligate intracellular parasites; however, they differ from viruses by being susceptible to antibiotics. Among the vertebrate host range of the chlamydiae are birds, mammals, and humans. The leading sexually transmitted disease in the United States is trachoma, caused by Chlamydia trachomatis; worldwide, it is the primary cause of human blindness. The most important occupational disease caused by the chlamydiae is psittacosis, a zoonotic disease caused by Chlamydophila psittaci. The primary reservoirs of C. psittaci are the psittacine birds (e.g., parrots) and domestic chickens and turkeys. Psittacosis is readily transmitted by aerosol, and the organisms remain stable in dried form for extended periods.

Bacteria

Bacteria are single-celled organisms. They have semirigid cell walls and a cell nucleus containing DNA that is not membrane bound. They reproduce through the process of binary fission. Bacteria include thousands of species, encompassing numerous genera. In addition to genus and species classification, bacteria can be categorized in several ways.

Morphologically, bacteria are categorized as cocci, bacilli, and spirilla. The cocci, which are round, spheroidal or ovoid in shape, are found as single cells, doublets, tetrads, clusters, and chains. The bacilli, or rod-shaped bacteria, occur as coccobacilli, square-ended bacilli, round-ended bacilli, club-shaped bacilli, and fusiform bacilli. The spirilla include the corkscrew and comma-shaped organisms (e.g., the vibrios and spirochetes).

Bacteria may also be differentiated based on the results of a commonly used differential specimen stain, the Gram stain. Organisms detected microscopically with this technique are described as Gram positive or Gram negative. Approximately 67% of the cocci and 50% of the bacilli are Gram positive. All spirilla are Gram negative. The mycobacteria (organisms that cause tuberculosis and atypical tuberculosis) have a waxy envelope and do not stain readily with the Gram stain. To detect mycobacteria, a special acid-fast staining procedure is required.

Bacteria may also be differentiated based on biochemical characteristics. Organisms may exhibit characteristic patterns of sugar fermentation and metabolic product formation. They may also require specific substrates or nutrients for growth.

Other techniques used to classify bacteria include bacteriophage typing (classification of bacteria based on susceptibility to different strains or types of species-specific viruses) and bacterial chromosome analysis using restriction endonucleases.

All Gram-negative bacteria possess a lipopolysaccharide component of the cell wall that displays toxic properties. This is referred to as endotoxin. Although the potencies of endotoxins produced by different bacterial species vary, all endotoxins possess pyrogenic (fever-inducing) properties. In the occupational setting, exposure to aerosols contaminated with polluted water, animal feces, or soil can result in human exposure to endotoxins.

Fungi

Fungi are composed of molds and yeasts; some species exhibit dimorphic properties, growing as either molds or yeasts depending on the substrate and temperature. Although thousands of fungal species are found in nature, <100 species are responsible for all human and animal diseases, and less than a dozen species are responsible for the majority of human mycotic infections. Fungal diseases are classified as mycoses, mycotoxicoses, and allergies.

The mycoses can be localized or systemic. The occupational mycoses transmitted by the respiratory route include blastomycosis, cryptococcosis, histoplasmosis, and coccidioidomycosis, which have been implicated as a etiologic agents in laboratory-acquired infections. All of these fungi are natural inhabitants of the soil and become aerosolized when the soil is disturbed, as occurs during construction, demolition, and other earth-moving activities. Histoplasma capsulatum and Cryptococcus neoformans, the causative agents of histoplasmosis and cryptococcosis, have a predilection for growth in soils contaminated with bird droppings; they are often found in the vicinity of poultry houses and bird-roosting areas.

Mycotoxicoses are intoxications resulting from exposure to fungal toxins (mycotoxins). Although numerous mycotoxins have been identified, the best studied are the aflatoxins, elaborated by species of Aspergillus. Besides possessing mutagenic, carcinogenic, and teratogenic properties, the aflatoxins are acute toxins affecting various body organs. The substrates for these molds are extensive and include most agricultural products, for example, corn and peanuts in the United States. Rigid standards have been imposed by the US Department of Agriculture to control aflatoxin levels of these commodities.

Fungal allergies are represented by clinical cases of allergic rhinitis, hypersensitivity pneumonitis, and asthma. The allergic manifestation is not an infection per se, and fungal viability is not required to induce allergic disease, since mycelial fragments, dead spores, and other fungal debris can elicit a host response. Common aeroallergenic fungal genera include Cladosporium, Penicillium, and Aspergillus, among others. Clinical and laboratory findings indicate that building-related illness is sometimes due to the inhalation of mold-contaminated air, but so-called sick-building syndrome remains a poorly defined illness of unknown etiology.

Parasites

Parasites may be involved as etiologic agents of occupational infections as a result of travel to, or work in, endemic areas. Illnesses such as giardiasis and amebic infections can result from workplace exposure to contaminated water. Human parasites can be classified as the protozoa and the helminths. The protozoa are single-celled organisms composed of the amoebae, the ciliated protozoa, the flagellated protozoa, the malarial parasites, Toxoplasma gondii, and Pneumocystis carinii. The helminths are multicellular parasitic worms.

Parasites may have complex life cycles that involve sexual and asexual reproductive states. Parasites may also infect both intermediate and definitive hosts. For different organisms, humans may serve the role as intermediate host, definitive host, or both.

TRANSMISSIBILITY OF DISEASE

The recognized routes of human exposure to etiologic agents of disease include (i) the respiratory route, (ii) the oral route, (iii) the contact route, (iv) the parenteral route, and (v) transmission through arthropod vectors.

Etiologic agents of occupational disease are most frequently transmitted through the respiratory route. Aerosolized particles (bioaerosols) composed of infectious or airborne allergenic (aeroallergenic) agents are difficult to detect or control. Exposure may result in sporadic and multiperson exposure in indoor and outdoor environments. The great majority of documented laboratory-acquired infections have resulted from apparent respiratory exposure, including disease agents not normally transmitted through aerosols (e.g., Rocky Mountain spotted fever and rabies). Bioaerosol particles, which measure 0.5–5.0 µm in aerodynamic size, can readily penetrate deep into the respiratory tract, reaching the alveolar spaces.

Occupational exposure to infectious agents through the oral route occurs by the following mechanisms: sprays and splatters, ingestion while mouth pipetting, consumption of contaminated foods, or touching the nose or mouth with contaminated hands. Since mouth pipetting has been prohibited in most laboratories, infection by accidental ingestion has been reduced significantly. Occupational infection by enteric pathogens, hepatitis A virus (HAV), listeria, and other agents continues to occur.

Contact exposure in the workplace has resulted in a variety of occupational infections, including tularemia, Newcastle disease, hepatitis B virus (HBV), human immunodeficiency virus (HIV), brucellosis, anthrax, glanders, erysipeloid, herpes, and leptospirosis. Transmission of disease organisms has occurred by contact with contaminated surfaces or fomites, exposure of mucous membranes and skin surfaces (including nonintact skin), and exposure to spatters and sprays of infectious agents. Routine handwashing practices and the use of gloves and other protective apparel can significantly reduce the spread of infectious organisms by contact.

Parenteral exposure to infectious organisms in the workplace results primarily from accidental needlestick or other penetrating trauma, such as skin puncture with sharp instruments or animal bites and scratches. Most workplace infections with HBV or HIV are the result of accidental needlestick or sharps injury.

Arthropods may serve as vectors in transmitting occupational infections. Examples of vector-borne diseases include the mosquito in malaria and the encephalitides, the flea in plague and tularemia, and the tick in Rocky Mountain spotted fever and Lyme disease. This route of infection is primarily associated with outdoor work, including forestry management and lumbering, agriculture, construction, and recreation management. Employees involved in outdoor activities and fieldwork need to be cognizant of vector-borne diseases, especially in endemic areas.

INFECTIVITY OF DISEASE

Following exposure to etiologic agents of disease, the infective process depends on a number of factors—namely, the resistance or susceptibility of the host, the exposure route and dose, and the virulence of the specific pathogen. Although host susceptibility is difficult to document, certain factors are recognized as being contributory, including age, race, gender, health status, underlying disease, pregnancy, vaccination status, and immunosuppression. The infectious dose varies significantly for different diseases, ranging from a single cell to millions of organisms. Moreover, the infectious dose differs by many orders of magnitude when exposure to the identical disease agent occurs through different routes of exposure. Exposure of nonhuman primates to Francisella tularensis, the causative agent of tularemia, results in disease with respiratory exposure to ~10 organisms. In excess of 100 000 are required to initiate disease when exposure occurs by ingestion. Additionally, although the infective dose of the blood-borne pathogens HBV and HIV are unknown, the significantly higher concentration of HBV in body fluids may be associated with the documented higher workplace infection rate of HBV. From the viewpoint of risk management, those pathogens that possess low infectious doses (e.g., tuberculosis, which has an infective dose of one tubercle bacillus) require a considerably higher level of infection control practices in the workplace.

Following exposure to disease-causing organisms, the infective process may lead to clinical, subclinical, or asymptomatic disease, which occurs after an incubation period of several days to several months. Clinical disease, associated with hallmark signs and symptoms, often begins abruptly with elevated temperature and general malaise, whereas subclinical infections are generally milder, of shorter duration, and associated with fleeting symptoms. However, with most diseases, the majority of those infected experience asymptomatic disease. These persons are completely devoid of clinical symptoms and any outward appearance of illness. The diagnosis of clinical disease is aided by the presence of clinical findings, whereas asymptomatic disease is usually only recognized through specific serologic tests. The process of seroconversion and elevation in specific antibody titer represents important criteria in the screening of employees for occupational exposures to infectious organisms. Workplace monitoring of employees for asymptomatic disease has provided invaluable information on infections such as tuberculosis and the hemorrhagic fevers.

Although many infectious diseases are transmitted to humans by a primary route, some are transmitted by several routes. Thus, it is generally recognized that tuberculosis is transmitted via aerosol, HAV by ingestion, erysipeloid by contact, rabies by penetration, and Lyme disease by a tick. However, in some occupational settings, especially in diagnostic, research, and production facilities, employees may be exposed to pathogens by abnormal routes, thereby leading to infectious diseases with puzzling clinical symptoms. Moreover, because large concentrations of etiologic agents are grown and manipulated in these workplaces, the opportunity exists for doses far exceeding community exposures. Thus, in workplaces where large quantities of infectious agents are being used, vigilance must be exercised to prevent human exposures via abnormal routes or with an overwhelming exposure dose.

Opportunistic infections occur in individuals, whose normal resistance to infection has been compromised, thereby making them susceptible to microorganisms that would not ordinarily cause disease. Those at higher risk include employees undergoing drug or steroid therapy resulting in transient immunosuppression and those with underlying disease associated with a permanent state of immunosuppression. Pneumocystis carinii infection in HIV-infected individuals and Aspergillus fumigatus infection in bone marrow transplant recipients are examples of opportunistic infections.

Zoonotic infections result from human exposure to animal diseases. There are more than 200 recognized zoonoses. Data on laboratory-acquired infections have demonstrated that many were zoonotic in nature and represented all classes of infectious agents. The transmission of zoonotic agents can occur in numerous occupations, including veterinary practice, agriculture, animal husbandry, and forest management. It also occurs in such workplaces as animal-holding areas, abattoirs, research laboratories, field operations, commercial fishing, and pet operations. It is imperative that specific infection control practices be instituted to protect workers from zoonotic infections, including the use of prophylactic vaccination, quarantine of feral animals, containment procedures, serologic screening, animal husbandry practices, vector management, and the use of personal protection equipment.

CLASSIFICATION OF MICROORGANISMS FOR LABORATORY WORK

The Centers for Disease Control and Prevention and National Institutes of Health (CDC/NIH) classification of biosafety levels for infectious agents is based on a combination of pathogenicity and transmissibility. Combinations of engineering controls, work practices, and personal protective equipment are recommended for each of the four biosafety levels (i.e., BSL1, BSL2, BSL3, and BSL4). The hierarchy of levels is based on the transmissibility of infectious agents by the aerosol route. For example, commonly used laboratory strains of E. coli, which are not virulent and not easily transmitted, are classified in BSL1. The blood-borne pathogens (e.g., HBV and HIV) are classified as BSL2 agents because they are not easily transmitted as aerosols but cause more serious and life-threatening disease. (For work with large quantities of these agents, such as viral cultures, they are classified as BSL3.) The aerosol-spread Venezuelan equine encephalomyelitis virus and the yellow fever virus, for example, are classified as BSL3 agents.

A related system of animal biosafety levels (ABSL-1 to ABSL-4) exists for work with research animals.

Further Reading

  1. Bennett JE, Dolin R, Blaser M, eds. Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Disease, 8th edn. Philadelphia: Elsevier Saunders, 2015.
  2. Chosewood LC, Wilson DE, eds. Biosafety in Microbiological and Biomedical Laboratories, 5th edn. HHS publication no. (CDC) 21-1112. Washington, DC: US Government Printing Office, 2009. Available at: http://www.cdc.gov/biosafety/publications/bmbl5/bmbl.pdf (accessed June 24, 2016).
  3. Willey JM, Sherwood LM, Woolverton CJ. Prescott’s Microbiology, 9th edn. New York: McGraw-Hill, 2014.

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