CEGE2008 Environmental pollution

PATHOGENS & MICROBIOLOGICAL

RISK ASSESSMENT

PATHOGENS

Objectives
1. To understand the difference between a pathogen and

non-pathogen

2. What the differences are between disease causing

organisms

3. Which pathogens are responsible for which diseases

4. How pathogens are transmitted
5. The measures that need to be taken to prevent

infections

Microorganisms/microbes
Bacteria

Protozoa

Virus

Algae

Fungi

Archaea

http://www.cellsalive.com/howbig.htm

Pathogens
An agent of disease. For example,

Bacillus anthracis is the pathogen

that causes anthrax.

A disease-causing agent. Most

pathogens are infectious microbes,

such as bacteria or viruses, which
are capable of causing disease.
Other parasites, such as fungi and
protozoans, are also considered
pathogens. Because not all
microbes are harmful, pathogens
refer specifically to those that can
cause disease or other harm.

Pathogenic microorganisms
Not all microorganisms are
pathogenic
Pathogens are found
among the:

Bacteria
Viruses
Fungi
Protozoa

Other non-microbe
pathogens:

Helminths & arthropods

Microbes as parasites
Other than viruses all
organisms are made up
of cells
Prokaryotic cells
smaller and simple
E.g. bacteria

Eukaryotic cells
larger, much more

complex and organised

E.g. protoza, fungi,
helminths, arthropods

Microbes as parasites
Classification
Each group is classified on the

basis of structural, functional

and genetic similarities
Most organisms are named
using the binomial (genus &
species) nomenclature:
E.g. Escherichia coli

Viruses are an exception with

strains named according to

types and variants

E.g. Influenza A virus subtype

H1N1

DNA viruses

Gram positive bacteria

Classification

Bacteria
Single-celled prokaryotes
One circular chromosome
Complex cell wall

Gram positive or Gram negative

Relatively few bacterial species

are pathogenic
Reproduce by binary fission
Wide range of metabolic patterns
(aerobic & anaerobic)
Some bacteria form endospores
to survive adverse conditions

Viruses
Carry genetic information
DNA/RNA encased in a

protein capsid
Cannot reproduce alone

Infect all forms of life, but

have specific host range

Active, latent or reactivated
Can be controlled by
vaccines

Fungi
Eukaryotic but distinct from

plants and animals

Thick carbohydrate cell wall
Filamentous or single celled
(yeasts)
Pathogenic species invade
tissues, digest material using
extracellular enzymes, then
take up nutrients from host
tissue
Fungal infections are known
as mycoses

Entamoeba histolytica

Protozoa
Single-celled animals
Multiply in the host until

controlled by the immune

system or treatment
Can cause particularly severe
disease in the
immunocompromised
Can cause disease directly but
pathology is more often caused
by the hosts immune response
Infections most common in
tropical and subtropical regions
Malaria is the most severe global
problem

Plasmodium vivax lifecycle

Helminths

The term is used for all parasitic worms

Tapeworms and flukes have a flat body and
muscular suckers/hooks for attachment to the
host
Roundworms have cylindrical bodies and no
specialised attachment organs
Generally large and complex organisms
Most common in warm counties
Many helminths have complex life cycles

Larval flukes and tapeworms must pass through one or

more intermediate hosts
Roundworms can develop to maturity in one host

Diseases are long lived and can last for many years
Transmitted in four distinct ways:

Via intermediate host

Faecal-oral route
Active skin penetration
Injection by blood-sucking insect

Taenia solium

Arthropods
Arguably most successful animals
Most important to human health

Mosquito

are:

Insects
Ticks
Mites

Adapted to live on humans

Use blood and tissue fluids as food
Can transmit microbial disease

through feeding habits

Those acting as intermediate
hosts can transmit helminth
parasites
Can also inflict dangerous bites

Tick

DISEASE TRANSMISSION

Transmission of disease
Diseases can be classified

according to their routes of

transmission:
Waterborne
Foodborne
Air-transmitted
Vector-transmitted
Sexually-transmitted
Other contact

Waterborne diseases
Different types of water and
sources of contamination:
Potable
Graywater
Leachate

Routes of infection:
Ingestion
Contact
Inhalation
Fecal-oral route

Waterborne diseases
Cholera

Causes severe diarrhoea and

vomiting
Caused by bacterium Vibrio
cholerae
Bacteria reproduce in the small
intestine and produce an
enterotoxin that triggers the host
response
Can lose fluids very quickly and die
within hours
Must provide fluid replacement
Not common today better water
purification measures
Haiti earthquake 2010

Vibrio cholerae

Waterborne diseases
Typhoid fever

Fever, followed by abdominal pain

and diarrhoea
Caused by bacterium Salmonella
typhi
The bacteria first enter the
digestive system
They quickly multiply, triggering
the initial symptoms such as a high
temperature, abdominal pain and
constipation or diarrhoea
If not treated, the bacteria will
spread into the bloodstream,
intestines, liver and bone marrow
Not common today better water
purification measures

Salmonella typhi

Foodborne diseases
Mostly bacterial:
Bacterial food poisoning
Ingestion of microbial
toxins microbe may not
even be present
Bacterial infections
The organism is present in
ingested food and then
parasitises the host to
produce disease

Foodborne diseases bacterial food poisoning

Staphylococcus aureus

Staphylococcus aureus

Often present on the skin

easily transferred to food

Food must be properly
refrigerated
If not, organism grows and
produces enterotoxin
Provokes sever diarrhoea and
vomiting within 1-6 hours

Clostridium botulinum

Spore former that is often

present in soil and sediments

Food must be thoroughly cooked
Bacteria produce neurotoxins
that can be fatal - botulism

Clostridium botulinum

Foodborne diseases bacterial infections

Salmonella spp.

S. typhimurium & enteritidis

Often harboured by chickens
Meat and eggs must be thoroughly

cooked
Sudden onset of fever, cramps,
diarrhoea and vomiting 12-48 hours
after eating contaminated food
Still very common

Toxigenic Escherichia coli

Many E. coli strains in human gut

Some produce enterotoxin
Some strains cause cramps and

diarrhoea
Some cause internal haemorradges and
kidney damage - enterohaemorrhagic
E. coli (Spanish cucumbers in 2011)

S. typhimurium

E.coli

Air-transmitted diseases
Infected host releases

aerosol droplets

Sneeze 20000 droplets

Cough 100s of droplets
Talking few droplets

Re-inhaled by new host

10 m trapped in nasal mucosa
1-4 m inhaled into lower

respiratory tract

Usually respiratory tract is

infected due to mode of

entry

Air-transmitted diseases
Tuberculosis

Bacterium Mycobacterium tuberculosis

Aerosols or dust are inhaled deep within

the lungs
The bacteria generally colonise
respiratory surface tissue
Build tubercles through which host O2
must pass providing O2 for the bacteria
Antibiotics can be used to treat TB, but
resistant strains are emerging
WHO has declared TB as a global
emergency

In 2011, 8.7 million people fell ill with TB

and 1.4 million died from TB
Over 95% of TB deaths occur in low- and
middle-income countries, and it is
among the top three causes of death for
women aged 15 to 44

Mycobacterium tuberculosis

Air-transmitted diseases
Influenza

Influenza virus many strains

Enters the respiratory system and

infects the host

Results fever, headache, mucus,
cough
Virus regularly undergoes genetic
reassortment mix of human and
animal strains
Swine flu epidemic in 2009-11

Influenza circulates worldwide and

can affect anybody in any age group

Influenza causes annual epidemics
that peak during winter in temperate
regions

Influenza virus

Swine flu

Vector-transmitted diseases
Transmitted from one

host to another via

another organism
Insect bites pick up
infection from host
bloodstream and inject
into the new host
E.g. mosquitoes
Stagnant water
Pesticides

Mosquito larvae

Vector-transmitted diseases
Malaria

Protozoan parasite Plasmodium

spp. transmitted by female

mosquitoes
Infection travels to liver, where
the protozoan reproduces and
then enters the bloodstream
Symptoms of fatigue, anaemia
and fever
Quinine used for years but
resistant strains are appearing
Vector control is the main way to
reduce malaria transmission - can
reduce transmission to close to
zero
219 million cases of malaria in
2010 and an estimated 660 000
deaths

Plasmodium

Vector-transmitted diseases
Plague
Bacterium Yersinia pestis
Bubonic (lymph nodes), pneumonic

(lungs) & systemic (whole body)

Buboes at lymph nodes, fever,
haemorrhage
Death in 3-5 days
Transmitted by rat flea
Epidemics in the middle ages
repeatedly killed of the
population
Now easily treatable by antibiotics
Still prevalent in some areas of the
world with occasional outbreaks

Yersinia pestis

Vector-transmitted diseases
Bacterial

Typhus fever

Ricketsia prowazekii spread by lice

Tsetse fly

Lyme disease

Borrelia burgdorferi spread by ticks

Protozoan

Trypanosomiasis

Trypanosoma gambese spread by tsetse flies

Viral

Dengue

Dengue virus spread by mosquitoes

Yellow fever

Yellow fever virus spread by mosquitoes

Rabies

Rabies virus spread by animal bites

West Nile encephalitis

West Nile virus spread by mosquitoes

Lice

Sexually-transmitted
diseases

Chlamydia trachomatis

Bacterial
Chlamydia
Chlamydia trachomatis

Viral
HIV/AIDS

Human immunodeficiency virus

HIV

Other diseases transmitted

by contact
Baclillus anthracis

Bacterial:
Anthrax
Bacillus anthracis

Viral:
Ebola

Ebola virus

Ebola virus

Hospital acquired infections

These are generally bacterial infections
Passed around hospitals due to high

concentration of vulnerable patients

Cause blood and soft tissue infections,
surgical site infections and respiratory
infections
Many are resistant to antibiotics
Examples:

Staphylococcus aureus
Clostridium difficile
Pseudomonas aeruginosa
Klebsiella pneumoniae
Acinetobacter baumannii
Enterococcus faecalis

MRSA infection

C. diff colitis

DETECTION & QUANTIFICATION

OF PATHOGENS

Detection and quantification

of pathogens
Culture methods
Sample is cultured using

specialist media and grown

organisms are identified
and enumerated

Culture independent

methods

DNA/RNA from a sample

used to identify and

quantify organisms

Culture methods
Sample is cultured using

specialist media
After a period of growth
organisms are counted and
identified
Pros

Organism physiology can be

assessed

Nutrient use
Antibiotic resistance

Cons

Labour intensive
Time consuming

Culture methods
Aseptic technique is employed at

all times

Bunsen burner
Ethanol
All solutions and tools are sterilised at

121 C

Sample is diluted or concentrated

Sample is introduced to solid or

liquid medium
Inoculated media are incubated
for a period of time
Organisms are identified by
microscopy and physiological
tests

Culture methods
Direct microscopic counts

counts obtained microscopically using a known volume and a grid

of known dimensions

Pour and spread plate method

bacteria from a known volume of water is cultured on agar and

enumerated by counting

Membrane-filter technique

a known volume of water is passed through a small-pore-size

membrane filter. The bacteria are retained by the filter and these
are then cultured on agar and enumerated

Multiple-tube fermentation

based on the principle of dilution to extinction where counts are

reported as most probable number per 100 mL (MPN)

Culture independent methods

DNA/RNA is extracted from a

sample
NA is used to identify and
quantify the numbers of
particular organisms
Pros

Quick
Easy to perform

Cons

Not possible to perform

physiological tests
More expensive

Culture independent methods

DNA/RNA is extracted from a

sample
NA is manipulated using
various methods
These often involve the use
of DNA and RNA enzymes
E.g. polymerases, restriction

enzymes

The methods are based on

known DNA/RNA sequences

Used to identify and
enumerate organisms

Culture independent methods

Polymerase chain
reaction (PCR)
Amplifies a known

sequence from the

sample

Microarray technology
Identifies many known

sequences from a
sample

DNA sequencing
Identifies unknown

sequence from a sample

Use of indicator organisms

Ideally we would want to
determine the concentration
of all organisms present in a
sample, but this is impractical
Indicator organisms are
numerous and easy to culture
microorganisms used as
surrogates for the total
number of microorganisms
present
E.g. E.coli is used as an indicator

organism for faecal

contamination water

Reading
Mims Medical Microbiology. Eds. Goering,
Dockrell, Zuckerman, Roitt & Chiodini. Elsevier.
2013. 5th Edition.
Chapters 1-6

Environmental Biology for Engineers and

Scientists. Eds. Vaccari, Strom & Alleman. Wiley.
2006.
Chapter 12

http://wiki.camra.msu.edu/index.php?title=Quan
titative_Microbial_Risk_Assessment_%28QMRA
%29_Wiki