Key Terms - Microbiology

Curtin MEDI1000 unit content on mid-semester theory test

Normal flora

Microbes that naturally inhabit externally exposed sites of the body (e.g. skin, nasal passages, mouth, intestines)

Algae

Eukaryotic, photosynthetic microbe

Protozoa

Single-celled eukaryotic microbes

Fungi

Can be divided into two categories:

1. Moulds: multicellular, produce hyphae, and may reproduce sexually or asexually

2. Yeasts: unicellular, only reproduce asexually via budding

Bacteria

Single-celled prokaryotic microbe, and very small (~0.5-2µm x 0.5-5µm)

Viruses

Not cellular, smaller still (10-300nm)

Gram stain reaction

Gram positive organisms have a thick peptidoglycan layer and will be stained purple (via crystal violet stain)

Gram negative organisms have a thinner peptidoglycan layer and will be stained pink (via carbol fuchsin)

Types of stains

• Simple stain: all components are stained the same colour

• Differential stain: different structures or features are stained different colours

Bacterial motility

• Flagella: motile in water

• Pili: used in conjugation

• Fimbriae: able to adhere to anything

Types of flagella

• Monotrichous: one appendage

• Lophotrichous: multiple appendages in roughly the same site

• Amphitrichous: multiple appendages on roughly opposite sides of the organism

• Peritrichous: organism is covered in appendages

Bacterial endospores

Certain bacteria are able to make a copy of their DNA (+ cytoplasm) enclosed in a thick layer of protein. These endospores are resistant to heat, disinfectants, and may survive for years, enabling a bacteria to survive in unfavourable conditions

Binary fission

A single bacterial cell divides into two

Generation time

The time it takes for a cell/group of cells to double (1-2-4-8 etc)

Condition factors for ideal bacterial growth rely on…

TAMPON acronym:

• Temperature

• Atmospheric conditions (oxygen)

• Moisture

• pH

• Osmolarity

• Nutrients

Obligate aerobe

(Bacterial categorisation - atmosphere) organism requires oxygen to grow

Microaerophile

(Bacterial categorisation - atmosphere) organism requires low levels of oxygen to grow

Obligate anaerobe

(Bacterial categorisation - atmosphere) organism is unable to grow in the presence of oxygen

Facultative anaerobe

(Bacterial categorisation - atmosphere) organism can grow with or without oxygen (independent factor)

Carboxyphile/capnophile

(Bacterial categorisation - atmosphere) organism requires high levels of carbon dioxide to grow

Psychrophile

(Bacterial categorisation - temperature) organism grows best at low temperatures (~0-20ºC)

Mesophile

(Bacterial categorisation - temperature) organism grows best at moderate temperatures (~10-45ºC)

Human body temperature: 37ºC

Thermophile

(Bacterial categorisation - temperature) organism grows best at high temperatures (~45-85ºC)

Acidophile

(Bacterial categorisation - pH) organism grows best at low pH (0-5.5 - acidic conditions)

Neutrophile

(Bacterial categorisation - pH) organism grows best at neutral pH (~7)

Alkalophile

(Bacterial categorisation - pH) organism grows best at high pH (8.5-11.5 - alkaline conditions)

Catabolism

Energy released through the breaking down of chemical bonds

Anabolism

Energy consumed through the creation of chemical bonds

Redox reactions

Oxidation (reducing agent) electrons are lost

Reduction (oxidative agent) electrons are gained

Catabolism examples

• Glycolysis

• Fermentation

(Reliant on presence of oxygen)

Mutualism

Both organisms involved in the relationship benefit from the relationship

Commensalism

One organism involved in the relationship benefits, at no harm to the other organism

Parasitism

One organism involved in the relationship benefits at the expense of the other organism

Incubation period

Prodromal phase

Invasive phase

Decline phase

Convalescence of host

Host’s recovery from infection

Virulence

An organism’s disease-causing traits

(e.g. the production and release of toxins or enzymes, adherence factors, presence of haemolysins)

Microbial biofilm

Moist surfaces in nature which contain microbes, cellular debris and any extracellular matrices. Organisms within the film are more resistant to antimicrobial agents and chemical treatments, and must be physically removed

Types of growth media

• Selective media: only certain bacteria can grow (manipulation of growth conditions)

• Differential media: bacteria can be distinguished by colony morphology or media reactions

Microbial control methods

In order from least to most effective:

1. Cleaning (mechanical removal of visible soils)

2. Sanitisation

3. Disinfection (removes pathogens)

4. Sterilisation (removes all microbes)

Disinfection

Killing of pathogenic organisms

Chemical or physical methods

Examples of physical disinfection methods

Heat (e.g. pasteurisation)

Radiation (non-ionising UV light and infrared, ionising radiation)

Pasteurisation

Heating of items that require disinfection

1. Low temperature for a long time - used for heat-sensitive items

2. High temperature for a short time (e.g. destroys pathogens in raw milk)

(Pioneered by Lewis Pasteur in the mid 1800’s to prevent wine spoilage)

Radiation

• UV light damages proteins and nucleic acid, causing dimers (however has low penetrating power and must be used for a long time, as a surface treatment)

• Infrared also requires prolonged exposure

• Ionising radiation (via electron beams, gamma rays and x-rays) is used to treat food

Chemical disinfectants

Alcohols, aldehydes, halogens, heavy metals, phenols

Act through chemical antagonism, cell membrane disruption or protein coagulation/denaturation

Organic matter effect on disinfectants

Organic matter (e.g. blood and other human excretions) must be mechanically removed (cleaned off) before disinfectant is applied

Organic matter forms a precipitate with the disinfectant, reducing it’s effectiveness, or forms a protective coat over bacteria

Alcohol disinfectants

Ethanol/isopropanol used on surfaces and skin

They are not effective against spores and non-enveloped viruses

Aldehyde disinfectants

Formaldehyde, gluteraldehyde disinfectants used for objects only. They contain tissue fixatives which kill and preserve cells (e.g. formaldehyde is used to preserve cadavers)

Iodine (halogen) disinfectant

Effective against bacteria, fungi, some endospores and many viruses. Is slow release and has good residual activity

Chlorine

Broad spectrum disinfectant, which is corrosive at high concentrations (e.g. in bleach) and require long exposure time to be effective

» point to remember: when cleaning bathrooms, bleach is applied and then left to sit for a while

Clorhexidine

A skin antiseptic used as a pre-surgery scrub and clinical hand washing disinfectant

Factors affecting effectiveness of control methods

Size of microbial population, duration of use, concentration, temperature and pH, and whether certain microorganisms are able to resist treatment

Clinical asepsis

Achieved through handwashing before, between and after all patients, use of PPE and personal cleanliness, and disinfection and sterilisation of surfaces and equipment

Hierarchy of controls

1. Elimination

2. Substitution

3. Engineering controls (isolation)

4. Administrative controls

5. PPE

Face masks

PPE for mouth and nose, filters ~95% of 3µm particles

N95 respirator is more effective than surgical mask

Sterilisation

• Treatment in which all microbes are destroyed (INCLUDING endospores - this characteristic is used to test sterilisation effectiveness)

• Required in dressings, surgical implements, catheters, prosthetics and glassware

Autoclave

Sterilisation device that uses moist, hot air.

Biological strips made with endospores OR autoclave tape (Bowie-Dick testing tape) are used to test autoclave effectiveness

Dry heat sterilisation

Process done in a hot air oven/incinerator in a similar fashion to an autoclave, but with no moisture included - making it effective for powders which cannot get wet.

Gas and cold sterilisation

Using gas, a whole room may be sterilised (e.g. in containment/aseptic laboratories)

Cold rooms to keep items at low temperatures to denature microbial proteins

HEPA filter

HEPA - High Efficiency Particulate Air

Filter composed of multiple layers of randomly arranged fibres, and commonly used in biosafety cabinets and airplanes

A pre-filter must be used for larger particles so they don’t clog the HEPA filter

Antibiotics

Natural compounds that kill or inhibit other microbes

Synergism

When compounds act together

Antagonism

When compounds act against each other

Bacteriostatic

A compound that inhibits growth of microbes

Bactericidal

A compound that kills microbes

β-Lactam group

One of the largest antibiotic groups, that works by inhibiting the last stage of cell wall production (which eukaryotic cells don’t have)

β-Lactam ring structure must be intact for antibacterial activity

Some bacteria express β-Lactamase enzymes which give them resistance

Antibiotic resistance

Overprescription of antibiotics has led to overexposure, which creates a selective pressure which some bacteria are able to survive.

Through bacterial reproduction, the resistance is passed on to future generations.

Additionally, prolonged use of antibiotics can remove normal flora, leading to further infection

Phage therapy

Bacteriophages are viruses that target bacterial cells.

Administered through capsules, IV infusions or surface applications

Antifungal treatments

Fungi are eukaryotic, therefore it is hard to target as they have similar cell structures to humans.

Treatment is therefore long term and can be toxic

Antiviral chemotherapy

Viruses may be stopped/killed via:

• binding the virus in only one infected cell

• prevent uncoating

• inhibiting viral replication

• interfering with viral release

Mycology

Study of fungi

Saprophytes

Fungi that obtain nutrients from decaying organic material

Parasitic fungi

Pathogenic fungi

Ubiquitous fungi

Fungi that may be found everywhere in an environment

Fungi morphological groups

Moulds, true yeasts, yeast-like and dimorphic fungi

Septate hyphae

Hyphae appears segmented (non-septate would have no such appearance)

Sabouraud agar

A growth medium used specifically for fungi. Has high sugar levels, a low (acidic) pH, and antibiotics to suppress bacterial growth

Budding

Yeast-type fungi reproduce via budding - similar to cell division

Spores

Mould-type fungi reproduce either sexually or asexually via spores

Examples of asexual spores:

• Sporangiospores

• Chlamydospores

• Conidiospores (form as the hyphae tip)

• Arthrospores (form as part of hyphae)

• Blastospores

Superficial fungal infection

Forms on mucosa surfaces (candida) or skin (cutaneous infection - dermatomycosis e.g. ringworm)

Systemic mycoses

Begin as a lung infection and caused by a dimorphic fungal pathogen (e.g. histoplasmosis, blastomycosis)

Mycotoxins

25% of the world’s food is contaminated with mycotoxins, though these levels are usually too low to cause illness.

Some mycotoxins can be used as treatments, for example, ergotamine is used to treat migraines

Virus reproduction

Viruses are unable to reproduce outside of a host (obligate intracellular parasites), and therefore cannot be grown using synthetic media

Baltimore classification scheme

Viruses are classified based on their genome type/nucleic acid

Virion structure

• Nucleic acid core (DNA/RNA)

• Protein capsid (shape, protection, attachment)

• Some virions are enveloped

Virion morphology

Virions may be helical, icosahedral or complex (e.g. bacteriophages)

Modes of transmission

Physical contact (direct/indirect), airborne, foodborne, arthropod-borne, direct inoculation, intraplacental

Nematodes

Roundworms

Platyhelminths

Flatworms (e.g. liver fluke, cestodia)

Iatrogenic

Illness caused by medical practices/practitioners

Also - nosocomial (originates in a hospital)

Exogenous

Illness originates from the external environment

Endogenous

Illness originates from within the host

Congenital

Disease that passes from a mother to a newborn

Zoonoses

Disease transmitted between animals and humans
Could involve a vector

Vector

A carrier of a disease that is not affected by the disease

(e.g. mosquito)

Epidemiology

The study of the spread, frequency and distribution of diseases

Epidemic

A disease that becomes widespread within a community

Pandemic

A disease that spreads beyond one region/community

Sporadic

Widely scattered or occurring irregularly