Epidemiology Microbiology-242N

Epidemiology Microbiology-242N. Time to put on your epidemiology hat! Investigate and describe one disease outbreak (epidemic, endemic, sporadic, pandemic, etc.) in the last 200 years. Explain why the outbreak was classified as such. As an epidemiologist, how would you prevent this type of outbreak in the future?

For the first post make sure to start with the reservoirs of diseases and your understanding in details and then describe the epidemiology with the important terms and what they mean in terms that we learned in lecture for chap 13.

Chapter 13

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Microbe–Human Interactions

Lecture Outline

See separate PowerPoint slides for all figures and tables pre-inserted into PowerPoint without notes.

Colonization, Infection, Disease

Infection: A condition in which pathogenic microorganisms penetrate host defenses, enter the tissues, and multiply

Pathologic state: Cumulative effects of infection damage, disruption of tissues and organs, results in disease

Disease: Any deviation from health. Factors –Infections, Diet, Genetics, Aging.

Infectious disease: Disruption of tissues or organs caused by microbes or their products.

Exogenous: originating from outside body- environment, another person, or animal

Endogenous: already existing on or in the body-Normal biota or a previously silent infection

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Importance of Gut Biota-Differences in gut microbiome have been associated with risk for: Crohn’s disease, Obesity, Heart disease, Asthma, Autism, Diabetes, Moods

Include an array of bacteria, fungi, protozoa, and viruses

have a profound effect on human biology

Human cells contain 22,000 protein encoding genes; microbes that inhabit humans contain 8 million (HUMAN MICROBIOME PROJECT)

Preliminary results:

Human cells contain 22,000 protein encoding genes; microbes that inhabit humans contain 8 million

We have a lot of microbes in places we used to think were sterile

All healthy people harbor potentially dangerous pathogens, but in low numbers

The makeup of your intestinal biota can influence many facets of your overall health

Differences in the gut microbiome have preliminarily been associated with differences in the risk for:

Crohn’s disease

Obesity

Heart disease

Asthma

Autism

Diabetes

Moods

Disease:

Any deviation from health

Factors that cause disease:

Infections

Diet

Genetics

Aging

Relationships Among Resident, Transient, and Disease-Causing Microbes, and Human Host

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Resident Biota: Normal biota/ resident or indigenous biota or normal flora Large and diverse collection of microbes living on and in the body. Include an array of bacteria, fungi, protozoa, and viruses

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Acquiring Resident Biota

Benefits of normal biota: Prevent the overgrowth of harmful microorganisms. Development/ sustain immune system

Microbial antagonism: antagonistic effect “good” microbes have against intruder microorganisms

Skin and adjacent mucous membranes, Upper respiratory tract, Gastrointestinal tract, including mouth, Outer portion of urethra, External genitalia, Vagina, External ear canal, External eye (lids, conjunctiva)

Endogenous/Opportunistic Infections: Caused by biota already in the body.

Can occur when normal biota is introduced to a site that was previously sterile.

Weak Immune system-Age: very young/old, Genetic defects in immunity and acquired defects in immunity (AIDS), Pregnancy, Surgery and organ transplant, Chemotherapy/ immunosuppressive drugs , Physical and mental stress

Broad spectrum antibiotics

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Opportunistic pathogens: Cause disease when:

The host’s defenses are compromised

When they become established in a part of the body that is not natural to them

Endogenous infections: Caused by biota already in the body

Can occur when normal biota is introduced to a site that was previously sterile

Example: Escherichia coli entering the bladder, resulting in a UTI

Continued Colonization of the Baby Through Diet

Fetuses are seeded with normal microbiota in utero??

Exposure occurs during birth when the baby becomes colonized with the mother’s vaginal biota

Breast milk contains around 600 species of bacteria

Bottle feeding

Skin contact with people- staff, parents, grandparents

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A growing number of doctors and scientists believe fetuses are seeded with normal microbiota in utero

These microbes are important for healthy full-term pregnancies and healthy newborns

Sugars used by healthy gut bacteria

Breast milk may be necessary for maintaining a healthy gut microbiome in the baby

Will Disease Result From an Encounter Between a (Human) Host and a Microorganism?

Pathogen: A microbe whose relationship with its host is parasitic. Results in infection and disease.

True pathogens: Capable of causing disease in healthy persons with normal immune systems

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Primary Biosafety Levels and Agents of Disease

Biosafety Level	Facilities and Practices	Risk of Infection and Class of Pathogens
1	Standard, open bench, no special facilities needed; typical of most microbiology teaching labs; access may be restricted.	Low infection hazard; microbes not generally considered pathogens and will not colonize the bodies of healthy persons; Micrococcus luteus, Bacillus megaterium, Lactobacillus, Saccharomyces.
2	At least level 1 facilities and practices; plus personnel must be trained in handling pathogens; lab coats and gloves required; safety cabinets may be needed; biohazard signs posted; access restricted.	Agents with moderate potential to infect; class 2 pathogens can cause disease in healthy people but can be contained with proper facilities; most pathogens belong to class 2; includes Staphylococcus aureus, Escherichia coli, Salmonella spp., Corynebacterium diphtheriae; pathogenic helminths; hepatitis A, B, and rabies viruses; Cryptococcus and Blastomyces.
3	Minimum of level 2 facilities and practices; plus all manipulation performed in safety cabinets; lab designed with special containment features; only personnel with special clothing can enter; no unsterilized materials can leave the lab; personnel warned, monitored, and vaccinated against infection dangers.	Agents can cause severe or lethal disease especially when inhaled; class 3 microbes include Mycobacterium tuberculosis, Francisella tularensis, Yersinia pestis, Brucella spp., Coxiella burnetii, Coccidioides immitis, and yellow fever, WEE, and HIV.
4	Minimum of level 3 facilities and practices; plus facilities must be isolated with very controlled access; clothing changes and showers required for all people entering and leaving; materials must be autoclaved or fumigated prior to entering and leaving lab.	Agents are highly virulent microbes that pose extreme risk for morbidity and mortality when inhaled in droplet or aerosol form; most are exotic flaviviruses; arenaviruses, including Lassa fever virus; or filoviruses, including Ebola and Marburg viruses.

A system of biosafety categories adopted by the Centers for Disease Control and Prevention (CDC)-degree of pathogenicity , relative danger in handling these pathogens

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Virulence

Virulence: Degree of pathogenicity. Indicated by a microbe’s ability to: Establish itself in the host & Cause damage

Virulence factor: Any characteristic or structure of the microbe that contributes to toxin production or induction of an injurious host response.

Examples of Virulence factors

Slime layer- attachment to surface

Fimbriae- attachment to surface

Viral spikes- attachment

Capsules- hides from immune system (antiphagocytic)

Leukocidins- substances toxic to white blood cells (antiphagocytic)

Hemolysin- breaking down RBC

Coagulase- formation of clots of blood and plasma

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Infectious dose (ID): a minimum number of microbes required for an infection to proceed

Determined experimentally for many microbes

Microbes with a smaller infectious dose have greater virulence

Structures, products, or capabilities that allow a pathogen to cause infection in the host

Adaptations that a microbe uses to invade and establish itself in a host

Steps Involved When a Microbe Causes Disease in a Host

Portal of entry: Exogenous / endogenous

Exogenous- A characteristic route taken by a microbe to initiate infection

Skin (Nicks, abrasions, punctures, exoenzyme)or mucous membranes- digestive (food/drink), respiratory (largest number of pathogens enter through nasal, oral), urogenital (STIs all genitals)

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Pathogens That Infect During Pregnancy and Birth

A few microbes cross placenta and are spread by umbilical vein into fetal tissues

TORCH: common infections of fetus and neonate

Toxoplasmosis

Other diseases: syphilis, coxsackievirus, varicella-zoster virus, AIDS, chlamydia

Rubella

Cytomegalovirus

Herpes simplex virus

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The placenta is an exchange organ:

Formed by maternal and fetal tissues

Separates the blood of the developing fetus from that of the mother

Permits diffusion of dissolved nutrients and gases to the fetus

A few microbes cross the placenta and are spread by the umbilical vein into the fetal tissues

Other infections are transmitted perinatally as the child passes through the birth canal

Becoming Established: Step Two—Attaching to the Host

Adhesion:

binding between specific molecules on host and pathogen

Pathogen limited to only those cells/ organisms to which it can bind.

Klebsiella uses capsule

Viruses use spike to enter host cells

Escherichia coli, Neisseria gonorrhoeae- use fimbriae

Slime layer used to attach to surfaces

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Quorum sensing: Chemical communication between nearby bacteria critical to establishment of infection

Adhesion:

A process by which microbes gain a more stable foothold on host tissues

Dependent on binding between specific molecules on both the host and pathogen

A particular pathogen is limited to only those cells and organisms to which it can bind

Once attached, a pathogen can invade body compartments

Becoming Established: Step 3—Surviving Host Defenses

Phagocytes:

White blood cells that engulf and destroy pathogens by means of enzymes and antimicrobial chemicals- phagocytosis

Antiphagocytic factors:

Virulence factor used by pathogens to avoid phagocytes-capsules, Leukocidins

Circumvent some part of the phagocytic process

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Step Four: Causing Disease

Virulence factors:

Structures, products, or capabilities that allow a pathogen to cause infection in the host

Adaptations that a microbe uses to invade and establish itself in a host

Indirect damage-Determine the degree of tissue damage that occurs-interplay between microbe and host

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Many cases of microbial diseases are the result of indirect damage or the host’s excessive or inappropriate response to a microorganism

Pathogenicity is a trait not solely determined by microorganisms

Pathogenicity is a consequence of an interplay between microbe and host

Direct Damage via Enzymes

Exoenzymes:

Secreted by pathogenic bacteria, fungi, protozoa, and worms

Break down and inflict damage on tissues

Dissolve host’s defense barriers and promote the spread of microbes into deeper tissues

Examples:

Mucinase

Keratinase

Hyaluronidase

Hemolysin

Coagulase

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Origins and Effects of Circulating Exotoxins and Endotoxin

*A toxoid is an inactivated toxin used in vaccines.

**An antitoxin is an antibody that reacts specifically with a toxin.

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Toxin: A specific chemical product of microbes, plants, and some animals that is poisonous to other organisms

Exotoxin:

Secreted by a living bacterial cell to the infected tissues

Many types

Endotoxin: Lipopolysaccharide of outer membrane

Not actively secreted

Shed from the outer membrane

Only gram-negative bacteria

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Localized Infection

Microbe enters the body and remains confined to a specific tissue:

Boils, Fungal skin infections, Warts

Systemic Infection

When an infection spreads to several sites and tissue fluids, usually in the bloodstream, nerves or cerebrospinal fluid

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When an infection spreads to several sites and tissue fluids, usually in the bloodstream

Viral: measles, rubella, chicken pox, AIDS

Bacterial: brucellosis, anthrax, typhoid fever, syphilis

Fungal: histoplasmosis, cryptococcosis

Focal Infection

Exists when the infectious agent breaks loose from a local infection and is carried to other tissues

Mixed Infection

Several agents establish themselves simultaneously at infection site

Polymicrobial diseases: gas gangrene, wound infections, dental caries, human bite infections

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Examples:

Tuberculosis

Streptococcal pharyngitis: scarlet fever

Toxemia: infection remains localized, toxins are carried through the blood to the target tissue

Primary, Secondary Infections

Primary infection: Initial infection

Secondary infection: Occurs when a primary infection is complicated by another infection caused by a different microbe

Acute infections: Come on rapidly, have short-lived effects.

Chronic infections: Progress and persist over a long period of time

Acute versus Chronic Infections

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Signs and Symptoms: Warning Signals of Disease

Sign: Any objective evidence of disease as noted by an observer

More precise than symptoms-fever, chest sounds, Tachycardia, Abscesses, swollen lymph nodes, Septicemia, Microbes in tissue fluids, Skin eruptions, Leukocytosis Leukopenia

Symptom: Subjective evidence of disease as sensed by the patient.

Chills, Pain, ache, soreness, irritation, Malaise, Fatigue, Chest tightness, Itching , Headache, Nausea , Abdominal cramps, Anorexia (lack of appetite)

Syndrome: A disease identified or defined by a certain complex of signs and symptoms. AIDS

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Infections That Go Unnoticed

Asymptomatic, subclinical, or inapparent infections:

Host is infected but does not manifest the disease

Patient experiences no symptoms or disease and does not seek medical attention

Latency: A dormant state of an infectious agent

During this state, a microbe can periodically become active and produce a recurrent disease

Sequelae: Long-term or permanent damage to organs and tissues

Persistence of Microbes

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Vacating the Host: Step Five—Portals of Exit

Portal of exit:

Avenue for pathogens to exit the host

Secretion- coughing, sneezing

Excretion- urogenital tract, feces

Discharge

Sloughed tissue-skin.

Removal of blood

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Some intestinal pathogens cause irritation in the intestinal mucosa that increases the motility of the bowel

Resulting diarrhea provides a rapid exit for the pathogen

Helminth worms release eggs and cysts through the feces

Feces containing pathogens are a public health problem when allowed to contaminate drinking water or when used to fertilize crops

Respiratory and Salivary PortalsEscape media for pathogens that infect the upper and lower respiratory tract: Mucus, Sputum, Nasal drainage

The outer layer of skin and scalp is constantly being shed into the environment

Household dust is composed of skin cells

A single person can shed several billion skin cells a day

Blood has a portal of exit when it is removed or released through vascular puncture

Blood-feeding animals are common transmitters of pathogens:Ticks, Fleas, Mosquitoes

Stages in the Course of Infection and Disease

Incubation period -time from initial contact with infectious agent to appearance of first symptoms.

Prodromal stage- notable symptoms start

Period of invasion- Infectious agent multiplies at high levels, exhibits its greatest virulence, and becomes well established in its target tissue

Convalescent- symptoms decline, recovery.

Continuation- only some infections, chronic Lyme disease, typhoid

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The incubation period is the time from initial contact with the infectious agent (at the portal of entry) to the appearance of the first symptoms. During the incubation period, the agent is multiplying at the portal of entry but has not yet caused enough damage to elicit symptoms. Although this period is relatively well defined and predictable for each microorganism, it does vary according to host resistance, degree of virulence, and distance between the target organ and the portal of entry (the farther apart, the longer the incubation period). Overall, an incubation period can range from several hours in pneumonic plague to several years in leprosy. The majority of infections, however, have incubation periods ranging between 2 and 30 days. The earliest notable symptoms of infection usually appear as a vague feeling of discomfort, such as head and muscle aches, fatigue, upset stomach, and general malaise. This short period (1 to 2 days) is known as the prodromal stage. Some diseases have very specific prodromal symptoms. Other diseases have an imperceptible prodromal phase. Next, the infectious agent enters a period of invasion, during which it multiplies at high levels, exhibits its greatest virulence, and becomes well established in its target tissue. This period is often marked by fever

Living Reservoirs

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Reservoir:

Primary habitat in the natural world from which a pathogen originates

Human or animal carrier; soil, water, or plants

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Animal reservoirs- Zoonoses

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An infection indigenous to animals but also transmissible to humans

Human is the dead-end host and does not contribute to the natural persistence of the microbe

Spread of disease is promoted by close associations of humans with animals

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Carrier States

Carrier:

An individual who inconspicuously shelters a pathogen (asymptomatic) and can spread it to others without knowing

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Vectors

In epidemiology, a live animal that transmits an infectious agent from one host to another

Majority of vectors are arthropods

Biological vector: Actively participates in a pathogen’s life cycle. Serves as a site in which the pathogen can multiply or complete its life cycle

Mechanical vectors: Not necessary to the life cycle of an infectious agent, Merely transport the pathogen without being infected

Biological vectors are infected

Mechanical vectors are not infected.

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Nonliving Reservoirs

Microbes have adapted to nearly every habitat in biosphere

Soil, water, and air

Most are saprobic and cause little harm to humans

Some are opportunists

A few are regular pathogens

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Acquisition and Transmission of Infectious Agents

Communicable disease: infected host can transmit infectious agent to another host and establish infection in new host.

Contagious: agent is highly communicable, especially through direct contact.

Noncommunicable: Does not arise through transmission of the infectious agent from host to host.

Horizontal transmission: Disease is spread through a population from one infected individual to another.

Vertical transmission: Transmission from parent to offspring via ovum, sperm, placenta, or milk

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Patterns of Transmission in Communicable Diseases

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Indirect Spread

Vehicle: Any inanimate material commonly used by humans that can transmit infectious agents.

Fomite: An inanimate object that harbors and transmits pathogens.

Oral-fecal route: Fecal carrier with inadequate personal hygiene contaminates food during handling, unsuspecting person ingests it.

Water and soil : can be temporarily contaminated with pathogens that come from humans.

Air: Indoor air can serve as a support medium for the suspension and dispersal of respiratory pathogens via droplet nuclei (pellets of mucus and saliva are ejected from mouth nose)

and aerosols (Suspensions of fine dust/ moisture particles in air with live pathogens)

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Droplet nuclei:

Dried microscopic residues created when microscopic pellets of mucus and saliva are ejected from the mouth and nose

Fomite:

An inanimate object that harbors and transmits pathogens

Not a continuous source of infection

Healthcare-Associated Infections

Infectious diseases that are acquired or develop during a hospital stay or stay in another health-care facility

Rates of HAIs can range from 0.1 to 20% of all admitted patients.

Medical asepsis: Practices that lower microbial load in patients, caregivers, hospital environment.

Surgical asepsis: Ensuring all surgical procedures are conducted under sterile conditions

*2014 data indicate these have started to decline.

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Infection control officer:

Implements proper practices and procedures throughout the hospital

Charged with:

Tracking potential outbreaks

Identifying breaches in asepsis

Training other health-care workers in aseptic technique

Using Koch’s Postulates to Determine Etiology

Essential aim of study of infection and disease is determining etiologic agent (causative agent)

Robert Koch:

Developed a standard for determining causation of disease that stood the test of scientific scrutiny

Determined the causative agent of anthrax

Koch’s postulates:

A series of proofs that established classic criteria for etiologic studies

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Epidemiology: Study of Disease in Populations

Epidemiology:

Effects of diseases on the community

Study of frequency and distribution of disease and distribution of disease and other health-related factors in defined populations

Reportable diseases: diseases considered to be of great public health importance- malaria, hepatitis, anthrax. (https://wwwn.cdc.gov/nndss/conditions/notifiable/2019/)

Notifiable diseases

By law, some diseases must be reported to authorities

Other diseases are reported on a voluntary basis

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Centers for Diseases Control and Prevention

Responsible for keeping track of infectious diseases nationwide

Part of the U.S. Public Health Service, incidence and prevalence can be tracked.

Disease trends and areas can be identified

High-risk epidemics can be identified and dealt with as quickly as possible.

The CDC shares its statistics on disease with the World Health Organization (WHO) for worldwide tabulation and control

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Epidemiological Statistics

Prevalence of disease: Total number of existing cases with respect to the entire population

Incidence of disease: Measures the number of new cases over a certain time period

Also known as case or morbidity rate

Mortality rate: Measures the number of deaths in a population due to a certain disease

Index case: The first patient found in an epidemiological investigation

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More Epidemiological Terms

Endemic: An infectious disease that exhibits a relatively steady frequency over a long time period in a particular geographic locale.

Epidemic: Whenever a disease occurs at a greater frequency than normal for a population or area

Sporadic disease: Occasional cases are reported at irregular intervals in random locales

Pandemic: Spread of an epidemic across continents

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Propagated epidemic:

Results from an infectious agent that is communicable from person to person and is sustained over time in a population

Epidemiology Microbiology-242N

Epidemiology Microbiology-242N

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