Epidemiology and Public Health Microbiology
WEEK 2
Epidemiology – study of distribution and determinants of health-related states or events in specified
populations and the application of this study to control of health problems (study of occurrence,
causes and circumstances of disease)
Impact of infectious diseases:
Shaped development of human society
Killed more people than all wars combined
Remain a threat to humanity
History changing ideas about infection
Royal Society (1650) – experimental evidence required to determine truth
Jenner (1796) – smallpox vaccination, cross-protection from cowpox
Semmelweiss (1840) – washing hands drastically reduces number of women dying after childbirth
Pasteur - discovered evidence to support germ theory of disease, pasteurisation and vaccine for
rabies
Lister (1867) – surgical antisepsis
Koch (1882) – Mycobacterium tuberculosis causes TB and Koch’s postulates
Koch’s Postulates
1. Agent foud in every case of the disease
2. The agent must be isolated into pure culture
3. Inoculation of pure culture into healthy animal must produce same disease
4. The organism must be receoverd from inoculated animal
Establishes causation – the agent, and no other cause, is responsible for the disease
John Snow – Father of Epidemiology
1849 – Snow proposed ‘cholera reproduces in human body & spreads via contaminated food and
water’
1854 – Cholera outbreak in Soho: ~500 deaths in 10 days and final total 616 dead. Snow maps cases
which implicated the Broad St water pump
Importance of understanding the epidemiology of infection
Observation and hypothesis testing
Identification:
Of the syndrome
Of the casusative agent
Of its origin
Of transmission
Factors that influence transmission
Disease Investigation
Establish diagnosis
Identify specific agent
Describe according to person, place and time
Identify source of agent
Identify mode of transmission
Identify susceptible populations
Epidemic investigation
Define epidemic
Examination the distribution of cases
Look for combination of variables
Develop hypothesis
Test hypothesis
Recommend control measures
, Epidemiology and Public Health Microbiology
Transmission of an infectious does of viable organisms to a susceptible host. Patterns of spread vary
from point source, restricted transmission (vertical or horizontal). Transmission may occur from index
cases or reservoirs
Spread – efficiency of transmission is the number of organisms shed:
Stability in the environment
Number required to infect a new host (infective dose)
Virulence properties of the organism
Host’s activities
Case v Time Graph
Herd Immunity
Levels of heard immunity in community. Susceptible protected in an immune community. Little
infection an occur in a heard thus ow levels of pathogens are about.
Pathogen Factors Host Factors
Virulence factors Sex
Strain Age
Dose Nutritional status
Route of exposure Vaccination status
Underlying conditions
Diagnosis of Infection
Circumstances causing the infection:
Pathogen epidemiology – generally predictable
Identify transmission cycles which need intervention:
Whether prophylaxis to others is indicated e.g. meningococcus
Public Health Measures against vectors, carriers, reservoirs:
Blood donors (identify carriers of HBV, HCV, HIV)
Infectious healthcare workers
Prospective laboratory diagnosis of infection
Prospective patient screening
Antenatal maternal screen
Healthcare worker screen & vaccination
Features of lab microbiology diagnosis
Frequently do not know what is being looked for and need to test for as many as possible. Also need
to be alret to unexpected and unusual pathogens/findings and their consequences.
Time is essential – outbreaks change over time and samples need to be taken. Missed samples
hinder establishing ‘cause and effect’ and the sequence of events in outbreaks, or patient diagnosis
Specimen quantity is paramount – as complete a set of samples possible and accompanied by clinical
notes.
Specimen contamination by normal flora minimised
Sterile site specimens need to be uncontaminated
Specimens need to be genuinely from the site
Specimen collection ideally prior to antibiotics and unexposed to disinfectants
Specimens transported and processed without delay
Clinical specimen requests usually call for microscopy, culture and sensitives. Microscopy and
staining on specimen:
May indicate specimen quality and suitability
May show an infectious/inflammatory picture
May suggest organism identification, depending on setting
Isolation of causative agent allows:
, Epidemiology and Public Health Microbiology
o Identification of pathogen
o Strain typing for tracing transmission
o Antibiotic sensitivity testing
To maximise the sensitivity of bacterial culture:
Inoculate & incubate without delay
Isolation may benefit from a larger inoculum e.g. blood culture
Enrichment may be needed (liquid media selective for pathogen (inhibits others))
Use multiple media and incubation conditions:
o Covers aerobes and anaerobes
Non-culture methods of microbial diagnosis:
Antigen detection e.g. polysaccharide capsular antigens, pneuoccocus meningococcus
Nucleic acid detection (NAT) – PCR e.g. chlamydia in urine, herpes. NAT detects both living
and dead organisms
Whole genome sequencing
Toxin and metabolite detection e.g. clostridium difficile toxin
Serology (detection of host antibody response to infection) – IgM antibody (recent/current
infection) and IgG antibody (previous infection), used as a lag indicator
WEEK 3 – FOOD BORNE DISEASES
Cost of food poisoning
The food safety council estimates:
5,400,000 cases of food poisoning in Australia/ year
1.2 million visits to the doctor
300,000 prescriptions for antibiotics
120 deaths
2.1 million days of lost work
~$1.25 billion cost
Organisms and/or molecules responsible
Bacteria – pathogenic: infectious does, survive stomach acid, colonise or at least briefly associate
with gut
Bacterial toxins – ingested with food (bacteria responsible may no longer be detected); other toxins
are made in gut
Viruses – viable, infectious does, no lipid bilayer envelope
Parasites – toxoplasma gondi
Food poisoning involves disease acquired from food (separate from food spoilage). There are multiple
sources of food-borne pathogens:
Endogenous: in food e.g. salmonella
Environment e.g. bacillus cereus
Humans e.g. staphylococcus aureus
Food infections invole bacterial growth or at least organism survival in food. Factors affecting this are:
pH
[O2] – may be reduced by aerobic and facultative bacteria; or heating of large pots
Processing can enhance growth as it pools contaminated and uncontaminated ingredients
increasing nutrient availability.
Food intoxications – ingestion of pre-formed toxin in food (contamination & growth in pre-cooked
food). Usually brief incubation period (0.5-6 hrs), vomiting prominent and outbreaks can be large.
Often most important virulence factor for microbes producing toxins.
Toxigenic – capacity to produce. 2 classes of toxins:
1. Exotoxins – secreted from bacteria. Produced by both GP and GN. Soluble and diffusible
made of proteins (enzymes). Usually carried on plasmids or prophages and inflict cell damage
by inhibiting specific metabolic functions:
WEEK 2
Epidemiology – study of distribution and determinants of health-related states or events in specified
populations and the application of this study to control of health problems (study of occurrence,
causes and circumstances of disease)
Impact of infectious diseases:
Shaped development of human society
Killed more people than all wars combined
Remain a threat to humanity
History changing ideas about infection
Royal Society (1650) – experimental evidence required to determine truth
Jenner (1796) – smallpox vaccination, cross-protection from cowpox
Semmelweiss (1840) – washing hands drastically reduces number of women dying after childbirth
Pasteur - discovered evidence to support germ theory of disease, pasteurisation and vaccine for
rabies
Lister (1867) – surgical antisepsis
Koch (1882) – Mycobacterium tuberculosis causes TB and Koch’s postulates
Koch’s Postulates
1. Agent foud in every case of the disease
2. The agent must be isolated into pure culture
3. Inoculation of pure culture into healthy animal must produce same disease
4. The organism must be receoverd from inoculated animal
Establishes causation – the agent, and no other cause, is responsible for the disease
John Snow – Father of Epidemiology
1849 – Snow proposed ‘cholera reproduces in human body & spreads via contaminated food and
water’
1854 – Cholera outbreak in Soho: ~500 deaths in 10 days and final total 616 dead. Snow maps cases
which implicated the Broad St water pump
Importance of understanding the epidemiology of infection
Observation and hypothesis testing
Identification:
Of the syndrome
Of the casusative agent
Of its origin
Of transmission
Factors that influence transmission
Disease Investigation
Establish diagnosis
Identify specific agent
Describe according to person, place and time
Identify source of agent
Identify mode of transmission
Identify susceptible populations
Epidemic investigation
Define epidemic
Examination the distribution of cases
Look for combination of variables
Develop hypothesis
Test hypothesis
Recommend control measures
, Epidemiology and Public Health Microbiology
Transmission of an infectious does of viable organisms to a susceptible host. Patterns of spread vary
from point source, restricted transmission (vertical or horizontal). Transmission may occur from index
cases or reservoirs
Spread – efficiency of transmission is the number of organisms shed:
Stability in the environment
Number required to infect a new host (infective dose)
Virulence properties of the organism
Host’s activities
Case v Time Graph
Herd Immunity
Levels of heard immunity in community. Susceptible protected in an immune community. Little
infection an occur in a heard thus ow levels of pathogens are about.
Pathogen Factors Host Factors
Virulence factors Sex
Strain Age
Dose Nutritional status
Route of exposure Vaccination status
Underlying conditions
Diagnosis of Infection
Circumstances causing the infection:
Pathogen epidemiology – generally predictable
Identify transmission cycles which need intervention:
Whether prophylaxis to others is indicated e.g. meningococcus
Public Health Measures against vectors, carriers, reservoirs:
Blood donors (identify carriers of HBV, HCV, HIV)
Infectious healthcare workers
Prospective laboratory diagnosis of infection
Prospective patient screening
Antenatal maternal screen
Healthcare worker screen & vaccination
Features of lab microbiology diagnosis
Frequently do not know what is being looked for and need to test for as many as possible. Also need
to be alret to unexpected and unusual pathogens/findings and their consequences.
Time is essential – outbreaks change over time and samples need to be taken. Missed samples
hinder establishing ‘cause and effect’ and the sequence of events in outbreaks, or patient diagnosis
Specimen quantity is paramount – as complete a set of samples possible and accompanied by clinical
notes.
Specimen contamination by normal flora minimised
Sterile site specimens need to be uncontaminated
Specimens need to be genuinely from the site
Specimen collection ideally prior to antibiotics and unexposed to disinfectants
Specimens transported and processed without delay
Clinical specimen requests usually call for microscopy, culture and sensitives. Microscopy and
staining on specimen:
May indicate specimen quality and suitability
May show an infectious/inflammatory picture
May suggest organism identification, depending on setting
Isolation of causative agent allows:
, Epidemiology and Public Health Microbiology
o Identification of pathogen
o Strain typing for tracing transmission
o Antibiotic sensitivity testing
To maximise the sensitivity of bacterial culture:
Inoculate & incubate without delay
Isolation may benefit from a larger inoculum e.g. blood culture
Enrichment may be needed (liquid media selective for pathogen (inhibits others))
Use multiple media and incubation conditions:
o Covers aerobes and anaerobes
Non-culture methods of microbial diagnosis:
Antigen detection e.g. polysaccharide capsular antigens, pneuoccocus meningococcus
Nucleic acid detection (NAT) – PCR e.g. chlamydia in urine, herpes. NAT detects both living
and dead organisms
Whole genome sequencing
Toxin and metabolite detection e.g. clostridium difficile toxin
Serology (detection of host antibody response to infection) – IgM antibody (recent/current
infection) and IgG antibody (previous infection), used as a lag indicator
WEEK 3 – FOOD BORNE DISEASES
Cost of food poisoning
The food safety council estimates:
5,400,000 cases of food poisoning in Australia/ year
1.2 million visits to the doctor
300,000 prescriptions for antibiotics
120 deaths
2.1 million days of lost work
~$1.25 billion cost
Organisms and/or molecules responsible
Bacteria – pathogenic: infectious does, survive stomach acid, colonise or at least briefly associate
with gut
Bacterial toxins – ingested with food (bacteria responsible may no longer be detected); other toxins
are made in gut
Viruses – viable, infectious does, no lipid bilayer envelope
Parasites – toxoplasma gondi
Food poisoning involves disease acquired from food (separate from food spoilage). There are multiple
sources of food-borne pathogens:
Endogenous: in food e.g. salmonella
Environment e.g. bacillus cereus
Humans e.g. staphylococcus aureus
Food infections invole bacterial growth or at least organism survival in food. Factors affecting this are:
pH
[O2] – may be reduced by aerobic and facultative bacteria; or heating of large pots
Processing can enhance growth as it pools contaminated and uncontaminated ingredients
increasing nutrient availability.
Food intoxications – ingestion of pre-formed toxin in food (contamination & growth in pre-cooked
food). Usually brief incubation period (0.5-6 hrs), vomiting prominent and outbreaks can be large.
Often most important virulence factor for microbes producing toxins.
Toxigenic – capacity to produce. 2 classes of toxins:
1. Exotoxins – secreted from bacteria. Produced by both GP and GN. Soluble and diffusible
made of proteins (enzymes). Usually carried on plasmids or prophages and inflict cell damage
by inhibiting specific metabolic functions:
