Microbiology Module 10: Classification, Identification, and Epidemiology

Comprehensive practice vocabulary flashcards covering taxonomy, molecular diagnostics, host-microbe interactions, disease stages, transmission modes, and epidemiology based on Microbiology Module 10 lectures, reviews, and clicker questions.

Taxonomy

Grouping organisms into categories to show degrees of similarities.

Identification

• characterizing an isolate to determine the group to which it belongs

Classification

 arranging organisms into similar or related groups

Nomenclature

The formal system of assigning names to organisms.

Phylogeny

The study of the evolutionary history of organisms, showing relationships among organisms based on differences in conserved rRNA sequences.

Taxonomic Hierarchy

The organization of organisms into subdivisions from broadest to most narrow: Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.

Bacterial Species

A population of cells with similar characteristics.

Bacterial Strain

A variation within a population of cells of the same species, such as the non-pathogenic laboratory strain Escherichia coli K-12 versus the pathogenic strain Escherichia coli O157:H7.

Domain Bacteria

A domain of unicellular, prokaryotic cells that typically contain one circular chromosome, lack membrane-enclosed organelles, possess peptidoglycan in their cell walls, and evolved first from the original evolutionary branch point.

Domain Archaea

A domain of prokaryotic organisms that lack peptidoglycan in their cell walls, evolved after bacteria, and frequently thrive in extreme environments as methanogens, thermoacidophiles, or extreme halophiles.

Domain Eukarya

A domain comprising organisms whose cells contain a membrane-bound nucleus, plasma membrane, and mitochondria, subdivided into kingdoms Protista, Fungi, Plantae, and Animalia.

Bergey’s Manual of Determinative Bacteriology

A standard reference for bacterial identification based on cell wall composition, morphology, differential staining, oxygen requirements, biochemical testing, and environmental source or habitat.

Differential Staining

Staining procedures based on the chemical composition of bacterial cell walls, including Gram staining (Gram-positive vs. Gram-negative) and acid-fast staining.

Special Staining

Diagnostic staining techniques used to visualize specific bacterial structures, such as capsules, endospores, and the presence and location of flagella.

Biochemical Tests

Laboratory procedures that determine an organism's metabolic capabilities based on enzymatic activities, such as carbohydrate fermentation and the production of specific end products.

Rapid Identification Methods

Commercial test systems manufactured for medically important bacteria that perform multiple biochemical tests simultaneously, enabling identification within $24\,\text{hours}$ through numerical code profiling.

Antigenic

The property of microorganisms that stimulates a host's immune system to produce antibodies.

Antiserum

A solution containing known antibodies used in vitro to identify medically important microorganisms.

Slide Agglutination Test

A serological method in which unknown bacterial antigens in saline are mixed with known antiserum on a slide; positive identification is indicated by clumping (agglutination).

ELISA (Enzyme-Linked Immunosorbent Assay)

involves a reaction between known antibodies and an unknown bacterium. A serological test using known antibodies fixed in a 96-well microtiter plate to bind unknown antigens from patient serum, producing an enzymatic color reaction capable of differentiating bacteria to the strain level.

Western Blotting

• Used to identify antibodies in a patient's serum, these antibodies show previous exposure. A serological technique where known microbial antigen proteins are separated by electrophoresis, transferred to a membrane, and probed with patient serum to identify specific antibodies indicating previous exposure.

Phage Typing

Based on the fact that bacterial viruses attack only members of a specific species. A diagnostic identification method based on the high host specificity of bacteriophages, determined by inoculating a bacterial lawn and observing clear lysis zones (plaques).

Flow Cytometry

A technique where cells in fluid suspension pass through a laser beam to directly evaluate cell size, shape, density, and surface properties without requiring prior culturing.

Fatty Acid Profiles

A cellular profiling method widely used in clinical and public health laboratories that identifies bacterial species by separating and characterizing their unique fatty acid composition.

Nucleic Acid Hybridization

fancy word for base pairing: A-T or C-G. The greater the degree of hybridization, the greater the degree of relatedness

Typical cut off

if there is a difference of more than 10% GC between organisms, they are likely not related.

DNA Fingerprinting

• Used to determine the source of hospital-acquired infections 

• Treats DNA from different bacteria with the same restriction enzyme followed by separation of the fragments by electrophoresis to show a pattern

Polymerase Chain Reaction (PCR)

Can be used to increase the amount of microbial DNA to levels that can be tested by gel electrophoresis and is one method especially useful if the organism cannot be cultured

Reverse-Transcription PCR (RT-PCR)

• conversion of RNA to DNA

Real-Time PCR

can be detected as the reaction proceeds, can be quantitated, and is more specific.

Dichotomous

• (means cut in 2) identification is based on successive questions with only 2 possible answers 

• the answer to each question leads to another until the organism is identified

Cladogram

• Maps that show evolutionary relationships among organisms 

• Uses rRNA sequencing 

• 2 rRNA sequences are aligned and the percentage of similarity between it sequences is calculated

Symbiosis

A relationship between two organisms in which at least one organism is dependent on the other, encompassing mutualism, commensalism, and parasitism.

Mutualism

• both organisms benefit (ex. Escherichia coli in the large intestines) 

Commensalism

One organism benefits, and the other is unaffected (ex. Streptococcus pyogenes in the intestine) It may also be an opportunistic pathogen

Parasitism

• One organism benefits at the expense of the other (ex. influenza virus on a host cell)

Microbial Antagonism (Competitive Exclusion)

can benefit the host by preventing the overgrowth of harmful microorganism

Normal Microbiota

• microorganisms that are present under normal conditions but do not produce disease. They begin to be established at birth. Physical and chemical factors affect their growth. They are localized in specific body regions. They are present for a long time. 

Transient Microbiota

• microorganisms that are present for several days, weeks, or months and then disappear. They are the organisms we pick up in everyday life and are only temporary.

Opportunistic Microorganism

• takes the opportunity to cause illness. Do not typically cause disease in their normal habitat in a healthy person but may do so in a different environment. 

Pathology

The scientific study of disease, primarily investigating etiology, pathogenesis, and structural or functional bodily changes.

Etiology

• cause of the disease (1st concern)

Pathogenesis

• the manner in which a disease develops, its characteristics, and steps leading to the disease, how it impacts a human (2nd concern)

Infection

• the invasion or colonization of the body by pathogenic microorganisms 

Disease

• occurs when an infection results in any change from a state of health 

• An infection may exist in the absence of detectable disease 

Symptoms

• changes in body function (ex. Fatigue, achy) They are not measurable.

Signs

objective changes the physician can observe and measure (ex. Temperature, heart rate)

Syndrome

• specific group of symptoms or signs that always accompanies a particular disease 

Communicable Disease

• any disease that spreads from one host to another, either directly or indirectly 

Contagious Disease

diseases that are easily spread from one person to another

Noncommunicable Disease

not spread from one host to another (ex. Tetanus)

Incubation Period

• no signs or symptoms. Interval between initial infection and first appearance of signs or symptoms 

Prodromal Period

relatively short period in some diseases characterized by early, mild symptoms

Period of Illness

• disease is most severe (death can occur)

Period of Decline

signs and symptoms subside, but the patient is vulnerable to secondary infections

Period of Convalescence

• individual regains strength, and the body returns to its prediseased state (no symptoms are present in this period) 

• Spread of illness can occur from incubation through this period

Acute Disease

• develops rapidly but lasts only a short time (ex. Influenza)

  • illness is short term because the pathogen is eliminated by the host defenses, person is usually immune to reinfection 

Chronic Disease

• develops more slowly, and the body’s reactions may be less severe, but it is likely to continue or recur for long periods (ex. Mono)

  • illness persists over a long period of time 

Subacute Disease

An illness whose clinical onset and duration fall intermediate between an acute disease and a chronic disease.

Latent Disease

A condition in which the causative pathogen remains dormant or inactive within the host for an extended duration, later reactivating to produce disease symptoms (e.g., shingles).

Local Infection

• invading microorganisms are limited to a relatively small area of the body (ex. Boils and abscesses)

Systemic Infection

• microorganisms or their products are spread throughout the body by the blood or lymph (ex. Measles)

Focal Infection

• spread from one area to a specific location in the body (ex. From teeth)

Primary Infection

• an acute infection that causes the initial illness

Secondary Infection

• Caused by an opportunistic pathogen after the primary infection has weakened the body’s defenses 

Subclinical (Inapparent) Infection

• does not cause any noticeable illness

Sepsis

• toxic inflammatory condition from microorganism infection 

Septicemia

• infection from multiplication of pathogens in the blood

Bacteremia

characterized by the circulating presence of bacteria in the blood.

Toxemia

characterized by toxins circulating within the blood.

Viremia

characterized by viruses in the blood

• Koch’s Postulates:

• 1. Same pathogen must be present in every case of the disease 

• 2. Pathogen must be isolated from the diseased host and grown in pure culture

• 3. Pathogen from the pure culture must cause the disease when it is inoculated into a healthy, susceptible laboratory animal

• 4. Pathogen must be isolated from the inoculated animal and must be shown to be the original organism

• Koch’s postulates are…

1. microbe cannot be grown on lab media

2. disease has multiple causes

3. disease is caused by multiple organisms

4. pathogen can cause several conditions

5. illness does not produce signs or symptoms

6. no other known host (ethical concerns infecting humans)

Exceptions to Koch’s postulates are…

Epidemiology

science that studies when and where diseases occur and how they are transmitted in populations

Sporadic Disease

• occurs only occasionally (ex. Typhoid fever)

Endemic Disease

• constantly present in a population (ex common cold) 

Epidemic Disease

• if many people in a given area acquire a certain disease in a relatively short period (ex. Influenza) 

Pandemic Disease

• an epidemic disease that occurs worldwide (ex. Influenza and AIDS) 

Incidence

• number of new cases in a population during a particular time period (often one year). 

• Indicator of the spread of the disease. 

Prevalence

• Number of existing cases in a population at a specified time or over a particular time period. 

• Takes into account both old and new cases. 

• Indicator of how seriously and how long a disease affects a population. 

Morbidity

•  the incidence of specific notifiable diseases 

Mortality

• the number of deaths from a disease 

Fomite

A contaminated, nonliving intermediate inanimate object (such as a used tissue, towel, or doorknob) that mediates indirect contact transmission between an infected reservoir and a susceptible host.

1. Contact

2. Vehicle

3. Vector

three groups of transmission disease are:

contact transmission

• spread of a disease agent by direct contact, indirect contact, droplet transmission, and sometimes congenital transmission. 

direct contact transmission

• direct contact between the source and susceptible host 

congenital transmission

• mother to fetus or newborn at birth 

indirect contact transmission

• from reservoir to a susceptible host by means of a nonliving, or fomite.

Droplet Transmission

• microbes are spread in mucus droplets that travel only short distances (not considered airborne). 

Vehicle Transmission

• transmission of disease agents by a medium such as water, food, air, body, fluids, drugs, and IV fluids

Airborne Transmission

A category of vehicle transmission wherein infectious agents spread within dust or droplet nuclei that travel distances greater than $1\,\text{meter}$ from the reservoir to a susceptible host.

Waterborne transmission

•  spread by water contaminated with untreated or poorly treated sewage 

Foodborne transmission

• transmitted in foods that are incompletely cooked, poorly stored, prepared in unsanitary conditions, or cross contaminated

Fecal-oral transmission

• fecal contamination of water or food that is ingested 

Vectors

• living organisms (most important group are arthropods) that carry pathogens from one host to another. They also involve both mechanical and biological transmission

Mechanical transmission

passive transport on body parts

Biological transmission

•  saliva, defecating or vomiting during biting that enters the wound

Healthcare-Associated Infections (HAIs)

Infections that patients acquire while receiving medical care in a healthcare facility (historically termed nosocomial infections), caused by hospital pathogens, compromised hosts, and hospital transmission chains.

Herd Immunity

•  when many immune people are present in a community 

Emerging Infectious Diseases

Diseases characterized as new, evolving, or displaying escalating incidence over recent years with potential to expand, driven by evolutionary adaptations, environmental shifts, transportation, or public health breakdowns.