By Professor Omar Hasan Kasule Sr.



The interaction between human tissues and microorganisms is very complex. The most successful parasites do not destroy their human hosts. The profile of disease-causing microorganisms is changing. New agents are being discovered. Some old agents are being eradicated. New pathogenic effects are being discovered for old known agents. Some agents are undergoing changes in pathogenicity. Organisms like the influenza virus can avoid host immune defences because of their frequent antigenic shift. Many microorganisms like N. gonorrhea have developed resistance to antibiotics.



There are several approaches to classification of microorganisms: cellular complexity, method of transmission, ability to cause disease, and method of interaction with humans. According to cellular complexity microorganisms can be classified as pro-karyotes, eucaryotes, and viruses. Prokaryotes comprise bacteria, rickettsiae, and chlamydia. Eucaryotes comprise fungi, protozoa, and helminths. Viruses are chemical entities with only rudimentary functions of life.


Microorganisms can be classified according to the method of transmission. There are several methods of transmission: feco-oral, soil contact, water contact, skin contact, air transmission, contact with body fluids, and arthropod-borne transmission. Examples of organisms transmitted by the feco-oral metjhods are ameba, giardia, shigella, vibrio cholera, salmonella spp, hepatitis virus A&E, polio virus, and tapeworms. Examples of microorganisms transmitted by the soil are trichuris, ascaris, hookworms, strongyloides, and tetanus. Examples of microorganisms transmitted by water contact are schistosomiasis and guinea worm. Examples of microorganisms transmitted by contact with infectious skin rashes are chickenpox and smallpox. Examples of organisms transmitted by inhalation are measles, pertussis, diphtheria, and tuberculosis. The following microorganisms are transmitted by contact with infected body fluids: trachoma, syphilis, gonorrhoea, and HIV. Arthropod vectors transmit the dengue virus and the malarial protozoan.


Microorganisms can be classified according to their ability to cause disease. The following parameters are used: infectivity, virulence, pathogenicity, toxigenicity, and the infective dose. Microorganisms can be classified according to their mode of interaction with the human host as saprophytic, parasitic, and symbiotic. Saprophytes live on dead organic matter. Parasites are dependent on the human host either as harmless commensals or as pathogenic parasites. Obligate parasites cannot exist outside their host. Non-obligate parasites are able to pursue an independent existence of they cannot find a host. Symbiotic relations involve mutualism and are mutually beneficial. Normal flora is bacteria in the body described as opportunist pathiogens. They are found in the mouth, URT, GIT, urethra, vagina, and the conjuctiva. They are beneficial to the body by preventing colonisation by pathogens as well as vitamin K synthesis. Normal flora can become opportunistic infections when they are in unusual sites or in conditions of reduced immunity.






Viruses are obligate intracellular parasites. They take over and use the cell's metabolism for their own replication. They are most vulnerable during transmission to and from the host. Viral infections are recognized by detection of viral antigens or antibodies to viral antigens. Among the commonly used serological techniques are: neutralization, hemagglutination inhibition, complement fixation, fluorescent antibody, radioimmunoassay, and ELISA. Small amounts of viruses can also be detected by cell culture.



Normal healthy individuals have a lot of bacteria most of which are harmless normal flora that prevents colonization by pathogenic bacteria. Bacteria may produce pathogenicity by direct action on the tissues, producing toxins, proteases, and cytolysins. Bacteria adhere to specific sites on the cell and initiate damage of the cell wall and gain entrance to the interior of the cell. Enterotoxins act on intestinal villi to cause diarrhoea. Toxins produced by vibrio cholerae, clostridium, tetanus, diphtheria, and anthrax bacteria have various effects on body tissues. Bacteria can be destroyed in the blood stream before entering cells by humoral or cell-mediated immune defence mechanisms. Adherence to the cell wall may be blocked by antibodires. Bacteria have developed methods of avoiding desrruction both outside and inside the cell. Encapsulation provides protection against physical elements. Antibiotic resistance mediated by plasmids and other mechanisms protects against antibiotic effects. Diagnosis of bacterial infections is based on cultivation & identification, gram staining & microscopy, biochemical reactions, use of specific antibodies, and DNA hybridization.



Fungal infections are comparatively less common than viral, bacterial, protozoal, or helminthic infections. Fungal infection is usually by direct contact with the soil or inhalation from the air. Person to person transmission of fungal infections is rare, the exception being dermatophytoses. The route of transmission determines the form of disease. Cutaneous and muco-cutaneous infection follows direct contact with the soil. Pulmonary disease is due to air inhalation. Fungal infections are usually localized. Systemic infections are rare but could occur and in a severe form in cases of malignancy and other causes of immune deficiency. Fungi can cause disease on ingestion in food. Examples of fungal poisons, mycotoxins, are amanita phalloides, a type of mushroom, aflatoxins and aspergillus flavus. Diagnosis of fungal infection is difficult and is based on clinical or histological examination.



Protozoa are single-celled eucaryotic organisms widely distributed in the world in both parasitic and free-living forms. Protozoa have developed ways of avoiding host immune defenses but are prudent enough not to destroy the host on whom they depend. This explains the high prevalence of protozoal infections but low morbidity levels. The following are protozoal species that are epidemiologically most important: plasmodium, toxoplasma, and pneumocytes. Plasmodia cause malaria that is the most important protozoal disease in terms of mortality and morbidity. P. falciparum causes more mortality and morbidity and is more important epidemiologically than the 3 other plasmodial species: P.ovale, P. vivax, and P. malariae. Red blood cells with HB-S, HB-F, or G6PD deficiency have natural resistance to malarial infection.  T.gondi is another protozoal infection with a high prevalence with little clinical disease. P. carinii is wide-spread and has become important epidemiologically because it is an opportunistic infection complicating HIV/AIDS.



There are 3 types of helminths: flat worms also caled cestodes, flukes also called trematodes, and roundworms also called nematodes. Helminths are widely distributed in the world but most species are in the tropics. Helminths can reside in human hosts for years producing eggs or larvae. They however cannot complete their life cycle in the human host. They have to live in the soil or other hosts for part of the lifecycle. Helminths are transmitted by vertebrate or invertebrate vectors. Helminths that migrate in the blood stream or that invade tissues can elicit an immune response. Those that infest the intestines elicit no immune response. The most important helminths from the epidemiological perspective are: schistosomiasis, hookworm, strongyloides, echinococcus, tenia, and toxicara. Schistosomiasis is of major worldwide epidemiological importance. Hookworm by causing chronic blood loss is responsible for a lot of malnutrition. S.stercoralis can live freely but also as a human parasite being able to live asymptomatically in the human body for 30 years or more. Strongyloides commonly causes intestinal disease; pulomnary disease occurs but is rare. It is associated with severe morbidity and mortality in immune-compromised persons. The larval stages of the following helminths are of epidemiological importance: echinococcus granulosus causing hydatid disease, echinococcus multiocularis causing hydatid disease, tenia solium causing cysticercosis, and toxacara canis causing visceral larva migrans.




During part of its lifecycle, the microorganism passes from one human host to another. It can also pass from the outside environment to the human host and vice versa. In a group of diseases called zoonoses, transmission is from animal to the human host. It is most vulnerable to destruction during the stage of transmission to the host. Microorganisms can survive adverse conditions and be transmitted by living in reservoirs, persistence in spores, latency, and growing in the vector or an intermediate host. Reservoirs can be humans, animals, or the soil..  Clostridia are bacteria that can survive long periods in the soil in an encapsulated form. EBV and CMV are examples of microorganisms that survive for a long time in a latent form.



Some microorganisms survive in reservoirs until they can infect humans. These reservoirs are intermediate animal hosts required to complete the lifecycle. Reservoirs that do not get diseased are more dangerous for humans because eradication is more difficult. Diseases without reservoirs are easier to eradicate. This explains the eradication of small pox because it has no natural reservoir. There are about 150 zoonoses. Direct zoonoses require only one animal reservoir for example rabies, brucellosis, and trichnosis. Cyclozoonozes like the tapeworm require at least 2 vertebrate species to complete the life cycle. Metazoonoses like the schistosoma helminth and the yellow fever virus require an intermediate invertebrate host. Saprozoonoses like coccidiomycosis require an inanimate intermediary in addition to an animal reservoir.



Vectors are organisms that tranfer the microorganisms. The transmission may be mechanical (eg flies and cockroaches) or hematophangous (eg ticks, lice, fleas, mites). Hematophagous transmission involves growth and replication in the vector. Replication within the host increases the number of infective microorganisms and thus enhances the infection potential.



Transmission is described as common vehicle spread for example by water, air of food or as serial transmission when it is human to human, human to animal to human, or human to the environment to human. Transmission may be direct or indirect. Indirect transmission may be vehicle-borne eg by fomites, vector-borne (mechanical and biological) or airborne (droplets or dust). Infection can be exogenous or endogenous. Exogenous infection is from outside the body of the host. It can be from humans, transient or chronic carriers, or the environment. Endogenous infection is from within the body of the host. The phenomenon of auto-infection found in strongyloides and E.coli are examples of auto-infection.


Disease transmission may be horizontal or vertical; the horizontal being more common. Horizontal transmission is from one human to another. Vertical transmission is intra-uterine from the mother to the fetus. The natural portals of entry into human are the respiratory tract (common cold, influenza, measles, TB, whooping cough), the urogenital tract (gonorrhoea, syphilis, herpes, HIV), the alimentary tract (amebic dysentery, shigellosis, polio, and cholera), the mucous membranes, the skin, the placenta (rubella, syphilis, and HBV), and the parenteral portal (intravenious and sexual). The skin is a good natural barrier to infection but can be penetrated by insects, ticks, needles, and traumatic injuries. The chain of infection starts with the pathogen in the reservoir (case, carrier, animal). It goes out from a portal of exit and is transmitted to the portal of entry. It enters the new host where it is established to cause disease. 



Horizontal transmission may be direct or incirect. Direct horizontal transmission causes immediate infection and occur in 4 forms: direct contact with the skin by biting or touch (eg hookworm), inoculation of the micro-organism (eg STD), ingestion of the micro-organism in food, drink, or contact with fomites (eg E.coli), and aerial/droplet spread (eg measles). Indirect horizonal transmission may be airborne, vehicle-borne, or vector-borne. The involvement of an intermediate host or vector causes delayed disease. Air-borne infections are carried as microbial erosols for example TB, influenza, histoplasmosis, and legionellosis. Vehicle borne transmission is by contaminated materials or objects (fomites) for example toys, handkerchiefs, soiled clothes, beddings, food service utensils, surgical instruments, water, blood, milk, organs and tissues. The vectors may be arthropods (such as mosquitoes, fleas, flies, lice, and ticks), zoonoses, plants, or other vehicles. They transmit organisms either mechanically or biologically. Dysentary and polio are examples of mechanical transmission.


Biological transmission is more common than mechanical transmission. Arthropods transmit microorganisms from one animal to another with humans being only accidental hosts like in plague. Mosquitoes transmit yellow fever, dengue, and malaria. Flies transmit African trypanosomiasis, onchocerciasis, loaiasis, and leishmaniasis. Ticks transmit rock mountain spotted fever, relapsing fever, and Lyme disease. Fleas transmit plague, and murine tyohus. Lice transmit epidemic typhus and trench fever. Kissing bugs transmit Chagga’s disesse. Zoonoses are diseases of whose reservoirs are vertebrates animals and are transmitted to humans by accident for example plague, rabies, rocky mountain spotted fever. Antrhoponooses are diseases whose reservoirs are human for example measles. Plants can be vectors of disease when they are contaminated by micro-organisms and are eaten raw.



The vertical route of disease transmission is trans-placental transmission in utero. It is thought but not yet decisively proved that the following organisms can be transmitted vertically: ?CMV, ?toxoplasma, ?rubella, ?HSV, ?syphilis, ?TB, ?VZ.



We can predict microbial transmission using mathematical models that have been developed from empirical observations. The factors of transmission probability are: the infected host, the susceptible host, contact, and the parasite. The basic reproductive number, R0, is the number of contacts per unit time x transmission probability per unit time x duration of infectiousness. An approximate formula for the basic reproductive number is R0 = 1 + L/A where L = average lifespan of an individual in the population and A = average age at infection. The serial interval or generation time is the time between two generations of infection.



The concept of the communicable disease triangle simplifies discussion of communicable disease. The triangle consists of the agent, the host, and the disease. They interact among one another. Elements of the environment that affect disease transmission are: climate (temperature, rain, wind patterns), vegetation (swamps, forest, and desert), water sanitation, air pollution, excreta disposal, housing, occupation (farm, factory). Poor sanitation and crowding increase the transmission of microorganisms. Breeding places near homes, forest reservoirs, and soil help the survival of organisms and their vectors.




Humans can be hosts of microbial infection in the following forms: intermediate host, definitive host, ?reservoir host, and accidental host. Humans can also be in a carrier status. They can be healthy, incubational, convalescing, or chronic carriers. Healthy carriers remain free of the disease while transmitting it to others; for example polio is transmitted by healthy carriers. HIV and HBV can be transmitted by incubationary carriers who are infectious before symptoms and signs of disease appear in them. Typhoid is transmitted by convalescing carriers. The human host has mechanisms to prevent the establishment of infection. These include: seborrhoeic acid in the skin and vaginal glycogen that is metabolized by lactobacilli to produce lactic acid.



Susceptibility to infection is determined by age, heredity, gender, pregnancy, nutritional status, life-style and behavior, personal hygiene, and immune resistance.


Age determines disease risk at the extremes of life. The very young and the elderly are immuno-incompetent and are more likely to be infected and also to experience more severe disease. Polio, hepatitis A, and influenza are an exception to this general rule being less severe in the young. Influenza is definitely more severe in the elderly. Heredity determines immune resistance.


Gender differences have been observed for many diseases. The susceptibility and attack rates for some diseases also vary by gender. The variation may be due to behavior or may be biological. Females enjoy an immunological superiority that may partially explain their longevity. Some diseases like RSV are more severe in boys. Pregnancy is a state of  immuno-incompetence that favours infection. Childbirth is a period of increased susceptibility to genital tract infection.


The nutritional status affects immune competence. Under-nutrition in the form of protein energy malnutrition, PEM, or micro-nutrient deficiencies causes immune incompetence. Life-style and behaviour affect exposure to infectious agents. The type of food eaten and pets kept may determine what micro-organisms a person is exposed to. Personal hygiene is important in ridding the body of likely pathogenic organisms.


Immune resistance is the main barrier to infection by micro-organisms. Immunity may be natural (innate) or acquired. Natural immunity is non-specific and is based on cellular barriers (NK cells and phagocytes such as macrophages, polymorphs, and reticuloendothelial cells), mechanical surface barriers (skin, mucous membranes, cilia, the cough angf gag reflexes), physiological barriers (fever), chemical barriers (stomach acidity, acidity of vagina, hydrolytic and proteolytic enzymes in the saliva and intestines, and biologically active substances like enzymes, lipids, & interferon), and inflammation. Acquired immunity to disease, cell mediated or humoral, develops as children grow into adulthood. Immunocytes are either T or B lymphocytes whose progenitors are in the bone marrow. Acquired immunity may be active or passive. Passive acquired immunity is based on maternal antibodies or therapeutic intervention by use of immune serum, cytokinase, or anti-toxins. Passive immunity occurs when formed antibodies are given either transplacentally or by post-natal vaccination. Some infections do not occur in the first 6 months of life because of passive immunity due to maternal antibodies secreted into milk and colostrum. Immunization against such diseases is not effective before the age of 6 months. Adoptive immunization is still in the experimental stage; it involves transfer of immunocytes from one person to another. Active acquired immunity occurs when antigens are given to stimulate antibody production. The vaccine may be in the form of killed micro organism or its products, modified microorganism, or toxoid. Primary immune deficiency is due to hereditary disorders. Acquired immune deficiency is due to infection, cancer, drugs, malnutrition, and pregnancy.



Spread of infection (number of new cases) is determined by the number of infected persons in the population and the degree of contact between the infected and the susceptibles. The number of susceptibles in the population is increased by birth and in-migration. It is decreased by death of cases, increased immunity, and out-migration.



Fever is a non-specific immune defence mechanism that slows down the multiplication of the agent. Interferon blocks the intracellular multiplication of viruses.




Clinical severity can be described as mild, moderate, severe, and fatal.



Clinical manifestations are: asymptomatic, latent, sub-clinical, and clinical.



Natural history describes the evolution of the disease process starting from initial infection until cure or development of chronic sequelae. Four stages are described in natural history: the pre-pathogenesis stage is operation of the risk factors, the pre-clinical stage is when  disease is initiated but there are no symptoms or signs. The clinical stage is when symptoms and signs manifest. The chronic stage is when complications and permanent deformities occur. Three time periods are described in the natural history of disease: the incubation, latent, and communicability perods. The incubation period is from onset of infection to appearance of clinical symptoms. The latent period is from initial infection to infectiousness. The communicability period (infectious period) is the duration when the infected person is infectious.


Two time lines can be drawn to compare the simultaneous evolution of infectiousness and disease.



Latent Period

Infectious Period

Non-infectious Period


Incubation Period

Symptomatic Period

No disease Period


Infectiousness and disease are both shown starting at the same point in time, the point of infection. The latent period ends when the person becomes infectious (is can transmit disease to others). Persons in the early symptomatic period are not yet infectious. Some people with no clinical disease may still be infectious. The non-infectious period is reached when the victims are cured, dead, or removed from the population. The no disease period is reached when the victims are dead, removed from the population, become immune or carriers.



Conditions for a communicable disease epidemic: Three conditions are necessary for an epidemic to occur: the pathogenic agent, host susceptibility, and effective transmission. The agent may be new or may be increased in number resulting in an epidemic. Sometimes epidemics occur because of change in the virulence of the agent. An adequate number of susceptible people in the population must exist to sustain and propagate the epidemic. The proportion of the susceptible necessary for epidemic transmission varies with the communicability of the agent. Highly infectious organisms with high communicability will cause epidemics even if the proportion of the susceptible is high. An epidemic cannot occur unless there is an effective means of transmission between the source of the pathogen and the susceptible person (page 269 Jennifer L Kelsey et al Methods in Observational Epidemiology. OUP New York and Oxford 1996).

Types of epidemics of infectious disease: the pattern of disease can be described as epidemic, a temporary excessive incidence rate; a pandemic, a worldwide epidemic, or endemic, disease persistently present in a community. Common source epidemics can be point source (1 person) & extended source (2 persons or more). Propagated source are when several foci are established from the primary focus. The Stages of the epidemic are shown on the epidemic time curves: ascending phase, plateau, and descending curve. The epidemic stops when there are no more susceptibles in the population to be infected. An epidemic may be single or may be secular or seasonal. A single epidemic may be single source epidemic or a propagated source epidemic with secondary and tertiary cases. The index case among the primary cases is of special epidemiological importance if identifiable. Arbovirus infection exhibits seasonality that matches mosquito breeding seasons.



In 1760 Daniel Bernouilli was the first to use a mathematical model when he evaluated the effectiveness of variolation. In 1840 William Farr fitted a normal curve on quarterly smallpox data in England and Wales for the period 1837-1839. In Epidemiological models are essentially mathematical models that simulate the natural course of disease. They help understand transmission dynamics by simplifying complex phenomena. Modeling uses mathematics that is a very precise language of communication. Problems and assumptions can be stated exactly and clearly using mathematics.


The model includes the major factors that determine the infection. Such models help study disease dynamics to help plan interventions. The general formulation is as follows: {# infected in a unit time} = {# infected persons in the population} x {force of infection} x {proportion of susceptibles in the population}. This formulation is also referred to as the law of mass action. The force of infection is affected by the following factors: environment, biology, social, and economic. Some of the common parameters in models are: coefficient of transmission, basic reproductive rate of infection, threshold density of susceptibles, and critical community size. The transmission coefficient has two components: the rate of contact and the probability of transmission. The basic reproductive rate of infection is R0 = b x k x D where b is the risk of transmission per contact, k is the number of potentially infectious contacts per unit time, and D is the length of time a primary case remains infectious. It can be seen from the formula that R0 is affected by the coefficient of transmission, the period of infectiousness, and the density of the susceptibles. An approximate formula for the reproductive rate is R0 = 1 + L/A where L = the average life span of an individual in the population and A is the average age at infection. Eradication of the infection occurs when R0 < 1. The threshold density of susceptibles is given by 1/bD.


The models for epidemic differ from those for endemic situations. Most modeling is that of the natural course. Complete description of the natural course of disease includes mode and rate of transmission, course of disease in the individual, and social and demographic characteristics of the community. In addition to the natural course, the model can also simulate interventions in which case the following factors are included in the model: treatment, prophylaxis, isolation, environmental change, and socio-economic change. Epidemiological models are used for the following purposes: planning and evaluation, health strategies, epidemiological investigations, training and education. Planning and evaluation of control programs, including analysis of cost-effectiveness and cost-benefit, is made easier by a model. Epidemiological models can be used to understand the concept of herd immunity and its relation to the coverage of mass vaccination programs. Epidemiological models can be validated using serological surveys. Use of saliva instead of serum makes such surveys easier and quicker. It must be noted hat not all the vaccinated develop immunity and that immunity wanes with time. The modeling of STDs differs from other infections because the rate is not correlated to population density and because of the carrier phenomenon.





The General control strategy consists of: Identification of cause, notification, treatment of cases using drugs, prevention, and surveillance. The differences between control and eradication are shown in the illustration. Only one infectious disease, smallpox, has been eradicated. Efforts are being undertaken to eradicate polio and dracunculosis. In the past several countries attempted tuberculosis and malarial eradication, some succeeded whereas others did not. Those that did not succeed did not have the resources needed for total eradication and they settled for strategies that would control and contain the disease without necessarily eradicating it completely. The complete eradication of small pox is one of the miracles of medical technology of this century. Three strategic approaches are used in infectious disease control: attacking the infectious agent at its source, interrupting transmission, and reducing the number of the susceptible population.


Control measures applied to the healthy host include active immunization, passive immunization, chemoprophyllaxis, behavioral change (sexual, dietary), physical isolation, and increase of host resistance by better nutrition and health care. If the host is already infected the following control measures are applied: chemotherapy, isolation, quarantine, restriction of activity, and behavioral change. Control measures applied to the vector include chemicals, environmental control, and biological control. Measures applied to animal reservoirs of disease include active immunization, restriction of movement or reduction in number, chemoprophyllaxis and chemotherapy. Measures applied to the environment include water sanitation, provision of safe drinking water, excreta disposal, and food sanitation. Measures applied to the causative agent include cleanliness, refrigeration, disinfection, and sterilization.


Disease notification plays a central role in disease control. The following are notifiable diseases according to CDC: AIDS, anthrax, botulism, brucellosis, cholera, congenital rubella syndrome, diphtheria, encephalitis, gonorrhoea, H. influenzae, Hansen’s disease, leptospirosis, lyme disease, measles, plague, paralytic polio, psitaccosis, rabies, syphilis, tetanus, trichnosis, tularemia, typhoid, and typhus. States notify CDC using the National Electronic Telecommunication System and CDC publishes the results in Morbidity and Mortality Weekly Report.



Primary prevention is prevention of initial contact and/or infection. Its objectives are elimination of the source by inactivating the agent, prevention of transmission, and raising the immunological status of the potential host. The agent can be inactivated by physical methods (heat, cold, or radiation) or by chemical methods (chlorination and disinfection). The chain of transmission can be broken by avoiding or destruction of animal and insect vectors and reservoirs including use of insecticides (adulticides, larvicides), repellents, personal protection eg mosquito nets, and biological control; environmantal control of air and dust; personal, domestic, and environmental hygiene; chemoprophyllaxis; detection and treatment of disease; quarantine and isolation; contact tracing; cooking and safe storage of food; safe drinking water; proper excreta disposal; good housing; quarantine and isolation. There are 4 types of disease isolation: strict isolation, contact isolation, respiratory isolation, and enteric isolation. Strict isolation requires a room with special ventilation and is used for pharyngeal diphtheria, viral hemorrhagic fevers, pneumonic plague, smallpox, varicella, and zoster. Contact isolation requires a special room with use of a face mask and is used for major wound or burn infections and acute upper respiratory infections. Enteric isolation requires special handling of waste and articles. .Host immune resistance can be increased by use of specific immunobiologics (active and passive immunization) or improvement in general health by nutrition and exercise.


Prevention may be targeted at the microbial agent (pathogen), the human reservoir, the portal of exit, the transmission chain, the portal of entry, and disease establishment in the new host. Pasteurization of milk, chlorination of water, anti-microbial drugs (antibiotics amf anti-viral) eradicate the agent and prevent further transmission. The human reservoir can be isolated or treated to prevent disease transmission. Transmission at the portal of exit is prevented by physical protection (mosquito nets, protective clothing, condoms, masks, insect repellents. Transmission from the reservoir towards a new host is interrupted by isolation, hand washing, vector control, sanitation, and sexual abstinence. Transmission at the portal of entry is interrupted by use of masks, condoms, and insect repellents. Establishment of disease in the new host is prevented by immunization, health education, nutrition, health promotion, and sexual abstinence.


Bacterial and viral diseases are generally immunizable whereas fungal and protozoal diseases are not. The goals of immunization are eradicating disease. More modest objectives are regional elimination of disease or control of disease by reducing morbidity and mortality. Immunization leads to both individual protection and increase of herd immunity. The minimum proportion of the population that must be immunized in order to achieve herd immunity is given by 1 – 1/R0 where R0 = basic reproductive rate. Immunization is of direct benefit to the immunized except in the case of rubella in which the offspring are the main beneficiaries. Large-scale vaccination programs result in an upward shift of the average age at infection due to the decrease in the proportion of the susceptibles being infected. In active immunization a vaccine is given to stimulate antibody production. The vaccines are in the form of live attenuated, Dead/inactivated, Active components, and toxoids (detoxified toxin). The primary IgM antibody response is seen in 1-3 weeks. The secondary IgG antibody response appears later but is permanent. In passive immunisation an already-formed antibody eg tetanus anti-toxin is given. In some disease immunization of animal reservoirs may be done in addition to human immunization.


The Expanded program on immunization (EPI), started in 1974, seeks to eliminate 6 childhood diseases: TB, diphtheria, tetanus, pertussis, polio, and measles. The effectiveness of vaccination programs is assessed based on the following factors: Effectiveness in prevention as assessed by morbidity and mortality, safety and efficacy as assessed by pre-license vaccine trials and post license monitoring, balance between need and risk, practicability, cost, uptake of vaccine and acceptability. Vaccine effectiveness (VE) is measured as the differences in attack rates in the vaccinated and un-vaccinated expressed as a proportion of the total number of the attack rate in the unvaccinated thus VE = (Incidence rate in unvaccinated – incidence rate among the vaccinated) / incidence rate in unvaccinated = 1 - RR. Field investigations relating to vaccination programs are carried out to achieve the following objectives: assessing the need for vaccination by analyzing morbidity and mortality data, pre-license and post-license monitoring, assessing vaccine efficacy by use of specific parameters, monitoring side effects of vaccines including the common and rare ones, assessing uptake and implementation of vaccination programs, evaluation of factors affecting vaccination programs, and costing studies The following parameters are used: disease incidence rates, immunological testing eg tuberculin test, seroconversion, and sero-prevalence. Community randomized, case control and follow-up studies can be employed in field investigations. Serological surveys can also be used to assess vaccination effectiveness. Failure of the vaccination program is indicated by lack of change in disease rates, increasing disease rates, or occurrence of disease in the vaccinated.


Immunization carries with it a relatively low risk of adverse reactions heavily outweighed by the disease preventive benefits. The rates of various adverse reactions to BCG vaccination are: disseminated infection <0.1 per 100,000; osteomyelitis <0.1-30 per 100,000; and suppurative adenitis 100-4000 per 100,000. The rates of various adverse effects to DPT immunization are convulsions 0.3-90 per 100,000; encephalitis 0.1-3 per 100,000; brain damage 02.-0.6 per 100,000; and death 0.2 per 100,000. Comparison of adverse effects in the DPT-immunized and non-immunized children in the following table makes the case for immunization. (page 374 John M Last Public Health and Human Ecology 2nd edition Prentice Hall International, Inc.):



Cases Per Million

Birth – 6 months

6 months – 5 years




















Residual Defect







NON-EPIDEMIC: Non-epidemic secondary prevention consists of diagnosing and treating cases. A non-epidemic situation can be treated as a problem to be resolved. The problem must first be ascertained to exist. Relevant literature on the subject is reviewed. Next techniques of descriptive epidemiology are applied by describing the time, place, and person characteristics of the problem. The problem is described using indicators of mortality, morbidity (incidence and prevalence), and disability. The end-result of epidemiological description is generation of hypotheses that can be tested using analytic epidemiology techniques that employ cross-sectional, case control, and follow-up study designs. In some situations experimental studies in animals or humans may be needed to answer etiological questions. The information collected must be assessed for bias and artifacts, validity, and reliability. Assessment must then be made for potential confounding effects on the purported etiological association. The final conclusion regarding causality is reached after considering the data using the criteria of causality: temporal sequence, strength of association, specificity, dose response, coherence, and consistency. Once the etiological relation is clear, preventive measures are undertaken. Understanding of the causal relationship and planning preventive approaches can be enriched by studying interaction or effect modification.


EPIDEMIC: In case of a community outbreak of an infectious disease, a systematic investigation is needed. The purpose of the investigation is to get information necessary for undertaking control and preventive measures. Clinical, epidemiological, microbiological, and laboratory evidence are combined to reach a conclusion on what measures to take. The processes involved in the investigation are: determining whether there is an epidemic by rapidly analyzing reports of cases; confirming the diagnosis of disease using clinical and laboratory criteria; agreeing on case definition; collecting data emphasizing the epidemiologic characteristics of time, place, and person; determining who is at risk of infection; and suggesting a hypothesis and testing it using available data or deciding to collect more systematic data. Practical plans of containing the epidemic are then drawn up based on conclusions from hypothesis testing. A report is written and mechanisms are set up for long-term surveillance and prevention.


Tertiary prevention: limit chronic disability by physiotherapy, supportive care, and surgical correction of deformities. Tertiary prevention for an individual aims at convalescence, recovery to full health, and return to normal activity. Tertiary prevention for the community aims at preventing the recurrence by disinfection and reapplication of primary and secondary preventive measures to prevent new cases of the disease.



An epidemic is an emergency situation. The problem is unexpected but immediate action must be taken. Investigations, deliberations, and detailed planning must of necessity be limited. Preparation for field investigation of a disease outbreak includes the following elements: selection and training of personnel, acquiring equipment, collaboration & consultation arrangements, setting up an efficient communication system, setting up an administrative structure, identifying the leader and defining the role of each member of the team. The investigation of an outbreak comprises socio-demographic information and information about the infection. Socio-demographic information is age, sex, occupation, and ethnicity. Information on the infection covers: identification of the cases, places of infection using a map, number of cases per time period, the source of infection, the mode of transmission, the people at risk of infection, and predisposing factors to infection rate of infection. Analytic studies (case-control or follow-up) as well as anecdotal observations are employed.


When the causative organism is known, drug treatment is usually needed. A choice is made between static and cidal drugs; cidal drugs are preferred. Drugs must have selective toxicity in that they kill the microorganism without harming the human host. If possible, drug choice should be preceded by sensitivity testing. If not possible, a broad-spectrum drug must be used. Antibiotics can be used for known infections and also for prophyllaxis of the susceptible. Drugs can cause toxicity, hypersensitivity, or harm the normal flora. Indiscriminate mass use of antibiotics should be discouraged because it leads to primary and secondary drug resistance (mutation & selection, plasmids). Cross-resistance can occur in some cases. Antibiotic prophylaxis can be pre or post exposure.


Other control approaches include quarantine, isolation, and disinfection. Post-outbreak surveillance: Serological, bacteriological, epidemiological, and clinical surveillance is carried out after the acute phase. Report of the out-break: At the end an epidemic report should be written showing the following main elements: causative organism, routes of transmission, epidemic curve, geographical distribution, clinical presentation, reason for the epidemic, and control measures used. The report serves the purposes of basic documentation for further action; record of what was done; medico-legal considerations; contribution  to scientific knowledge; and as a teaching tool.



The transmission cycle of respiratory infections is broken by reducing direct contact with the infectious source, isolation of serious infections, chemoprophyllaxis, and face masks. The transmission cycle of gastro-intestinal infections is by sanitation measures, fod hygiene, fly control, and personal hygiene. The transmission cycle of sexually transmitted diseases is broken by avoiding promiscuity and genital hygiene. The transmission cycle of vector-borne diseases is broken by chemo-prophylaxis and vector control (destroying breeding sites, prevent vector-host contact or access, and use of pesticides. The transmission cycle of zoonoses is by control of animal hosts. Immunization where applicable is a general measure of breaking the transmission cycle.




The reemergence of infectious diseases in the developed countries after falling over most of the 20th century is due to socio-demographic, lifestyle or human behavior, environmental, and medical technological factors. The socio-demographic factors are: demographic changes (aging, migration), wide scale commercial and tourist travel, increasing crowding especially in the large urban areas, behavioral and lifestyle changes are factors contributing to emerging infectious diseases. Some diseases are old diseases and are old problems. Some diseases are old but are new problems for example tuberculosis and malaria. Some are new diseases with new pathogens such as Ebola and HIV. The environmental factors are climatic changes (global warming, climate change, rising sea levels, heat waves, and ozone depletion) that disturb the eco-system and thus favor growth and transmission of old and new pathogens. Immune suppression in organ donation and nosocomial infections are side effects of medical technology.



Breakdown of traditional society and emergence of liberal ideas about sexual relations is behind the increase of STD. The traditional STDs are syphilis, gonorrhoea, and chanchroid. New diseases are chlamydia, genital warts, trichomonas, scabies, peduculosis, genital herpes, vaginal candidiasis, E. histolytica infection, G. lamblia, HVA, HBV, HCV, and HIV. Data on STDs is inadequate because of incomplete notification, non-uniform diagnostic criteria, and asymptomatic cases. Health education does not seem to be very effective in the prevention of STDs. Use of condoms by commercial sex workers is effective in decreasing STD incidence. Acquired Immunodeficiency syndrome (AIDS) appeared in 1981. The HIV 1 virus isolated in 1983 belongs to the retrovirus family. It attaches to the CD4+ lymphocytes which are depleted as the infection progresses. HIV is transmitted by semen, blood, vaginal and cervical secretions. Direct transmission occurs when contaminated syringe needles are shared by iv drug users, the perinatal period, breast milk, transfusion of blood and blood products, insemination with donated semen, transplantation of organs and tissues. Primary prevention consists of safe sex (monogamy or condom use), voluntary testing and contact tracing, safe blood supplies with use of antigen screening during the window between infection and appearance of antibodies, safe organ donation programs, precautions in medical facilities, and development of a vaccine.



The Marburgh virus disease was first recognized in Yugoslavia and Germany when people fell ill after contact with monkeys imported from Uganda. The Ebola/Marburg virus epidemic started in 1976 and has been recurring being imported into Europe and the US by importation of monkeys from Africa. The A swine flu epidemic was recognized in 1976. Lassa fever spread is favored by urbanization leading to rodent exposure in the homes. Travel, migration, and urbanization contribute to spread of dengue fever and dengue hemorrhagic fever. The Hantavirus pulmonary syndrome due to hanta virus associated with contaminated droppings of deer mice appeared in 1993. Hanta viruses are spreading because of ecological and environmental changes that increase contact with rodents. Hepatitis B and C are spreading due to transfusion, organ transplantation, intravenous drug abuse, and sexual transmission. Rift valley fever transmission is favored by dam building, agriculture, and irrigation. Yellow fever is being transmitted in new areas because of conditions that favor mosquitoes.


Streptococcus group A is an invasive necrotizing ‘flesh-eating’ bacterium whose increased transmission is not understood. The toxic shock syndrome due to infection of ultra absorbent tampons by Staphylococcus aureus appeared in 1980. Infections by enteropathogens such as Shigella are increasing. Cholera transmission is due to poor sanitation and introduction of new strains (such as O139) due to travel. The hemolytic uremic syndrome is due to mass food processing technology that allows Escheria coli O157:H7 to contaminate meat. Brazilian purpuric fever is due to a new strain of Hemophilus Influenzae. Helicobacter Pylori is probably not a new disease but has just been recognized as an association with gastric ulcers and other gastro-intestinal disorders. The decline of TB incidence in Europe and America registered in the 19th and 20 century due to socio-economic improvement started being reversed in the 1980s and 1990s due to bad social conditions (poverty, homelessness, and unemployment), infected immigrants, HIV infection, and rise of drug resistant TB. Control of TB is achieved by contact tracing, chemoprophyllaxis, and adherence to treatment schedules. Direct observed therapy (DOT) helps in ensuring treatment compliance. Shorter drug regimens also ensure that the problem of non-compliance does not arise. Prevention of TB is achieved by overall improvement in nutrition, social and environmental conditions, and alleviation of poverty. Primary prevention is based on BCG vaccination and chemoprophylaxis with INH which prevents reactivation of latent TB. Secondary prevention is treatment of multi-drug resistant conditions.


Malaria is spreading due to increasing travel and migration. Schistosomiasis is spreading due to dam building. Lyme disease due to a spirochete called borrelia burgdorferi appeared in 1975. Its transmission is aided by reforestation around homes that favors the tick vector and the deer, a secondary reservoir host. Legionnaire’s disease is due to a small infectious agent spread via air-conditioning systems appeared in 1976. Biofilms that form on water tanks and plumbing favor growth of the causative organisms. P. carinii and Cryptococcus spp are opportunistic infections. Cryptosporidium spp, Cyclospora spp and other water-borne pathogens are due to contaminated surface water and improper water purification.

Omar Hasan Kasule, Sr, Sep 2005