BIO203 Pathogenic Microbiology

Topic 1: Introduction & detection methods

(part 1)
2024- 25 SEMESTER 1
DR. XINZHAO TONG
Outline
Part 1
What are microbes?
Microbial pathogenicity
The etiology of infectious diseases
Part 2
How to determine which pathogen causes a disease?
Detection methods
Biological safety
What are microbes?

Are organisms only visible by microscope?

Megabacterium
Candidatus Thiomargarita magnifica, a sulfur-oxidizing bacterium
of grammaproteobacteria, has an average cell length of 10-20 mm.
Ca. Thiomargarita magnifica
Bacteria Eukaryote

Intracellular sulfur
granules

Under light microscope

CPR/DPANN
Ultra-small genome
• CPR -> Nanobacteria
• DAPNN -> Nanoarchaea

Symbiotic lifestyle

Cannot be cultivated independently

TM7 co-cultured with its bacterial host
Characteristics of microbes
Usually microscopically small
Genetically belonging to certain groups of species
Able to thrive in many environments, e.g.
◦ In the deep sea (dark, high water pressure)
◦ In dead sea (extremely salty)
◦ In hot springs (>80°C)
◦ Inside higher organisms
◦ In soil/water/air
◦ On plants
Extremophiles
Types of microorganisms
Microorganisms are found in each of the three domains of life: Archaea,
Bacteria, and Eukarya.

Microbes within the domains Bacteria and Archaea are all prokaryotes
(their cells lack a nucleus), whereas microbes in the domain Eukarya are
eukaryotes (their cells have a nucleus).

Some microorganisms, such as viruses, do not fall within any of the three
domains of life.
Domain

Kingdom

http://www.encognitive.com/node/10791
Main taxonomic ranks (M. furfur)
English Example
Domain Eukaryota
Kingdom Fungi
Phylum Basidiomycota
Class Malasseziomycetes
Order Malasseziales
Family Malasseziaceae
Genus Malassezia italicized
Species M. furfur
Why viruses are not included in the
phylogenetic tree?
 In a phylogenetic tree, the characteristics of members of taxa are
inherited from previous ancestors.
Viruses are excluded from the tree of life because they do not share
characteristics with cells, and no single gene is shared by all viruses or
viral lineages.
While cellular life has a single, common origin (monophyletic), viruses
are polyphyletic – they have many evolutionary origins.

https://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/
 Common bacterial shapes

Micrococcus Bacillus subtilis Vibrio casei Gardnerella Spirillum volutans Borrelia

luteus vaginalis burgdorferi

Coccobacillus is a combination of spherical (coccus) and rod-shaped (bacillus)

Types of symbiosis (=living together)
Mutualism: both members benefit from the
relationship (e.g., bacteria in human intestinal tract)
Amensalism: one population harms another but itself
remains unaffected (e.g., one produces bactericidal
substances that kill the others)
Commensalism: One benefits, the other neither
benefits nor is harmed (difficult to prove, but still used
a lot)
Neutralism: None of the organisms is affected in any
way
Parasitism: the parasite benefits whereas the host is
harmed by the relationship (Ustilago maydis on crops)
Human microbiome
Resident microbiota: microorganisms constantly present in or on the body (e.g. C.
acnes on skin)

Transient microbiota: microorganisms present temporarily and under certain conditions

- Hygiene and diet can alter both the resident and transient microbiota

Opportunists: are resident and transient microbiota that can cause diseases under
certain conditions or in certain locations in the body.
- opportunist pathogens
Resident microbiota
Resident microbiota varied by:
• body site
• skin physiology
• hygiene
• diet
• time
• antibiotic therapy

Resident microbiota are important for

human health because they occupy
niches that might be otherwise taken
by pathogenic microorganisms.
Human microbiome project
Launched by the U.S. National
Institutes of Health in 2007

Goals: understand the dynamics of

the human microbiome and the
relationship between the human
microbiota and diseases
Website: https://hmpdacc.org/

From population to individual

Focus of this module is on pathogenic
bacteria and fungi
“Good” microbes help us:
◦ Fermentation (cheese, wine)
◦ Penicillin and protein production
◦ NO2 fixation for plants
◦ Food for higher organisms (e.g. mushroom,
fruiting body of a fungus)
◦ Consume toxic waste
“Bad” microbes infect
◦ Animals including homo sapiens
◦ Insects (Ophiocordyceps  zombie ants)
◦ Plants
De Bekker, 2014
Microbial pathogenicity
Key concepts in pathogenic microbiology
Pathogen: a microbe that can cause disease
- Cellular (bacteria, parasites, and fungi) or acellular (viruses, viroids, and
prions).
Pathogenicity: the capacity of a pathogen to cause disease,
depending on its ability to invade a host, multiply in the host and
avoid being damaged by the defense mechanism of the host
Virulence: the intensity of the disease caused by a pathogen
(continuum, avirulent  highly virulent)
Attenuation: weakening of a pathogen’s disease producing capacity
(used in vaccines)
Indicators of virulence
Median Infectious Dose (ID50) and Median
Lethal Dose (LD50)
Animal models required

ID50: number of pathogen cells or virions

required to cause active infection in 50% of
inoculated animals
LD50: number of pathogenic cells, virions, or
amount of toxin required to kill 50% of infected
animals.
Contamination, infection & disease
Contamination: micro-organisms are present

Infection: multiplication of any parasitic organism within or on the

host’s body

Disease: a disturbance in the state of health wherein the body can

not carry out all its normal functions
Classification of infection
Local infection: a small area of the body, near the portal of entry (e.g.
abscess脓肿)
Focal infection: local infection that can cause subsequent infection or
symptoms in other parts of the body (e.g. tetanus破伤风)
Systemic infection: whole body through blood or lymph (e.g. chickenpox
水痘)
Primary and secondary infection
Primary infection, the initial infection caused by one pathogen, can lead
to a secondary infection by another pathogen

Patients infected with HIV  immunocompromised  more susceptible

to secondary diseases (e.g. tuberculosis 肺结核 and others caused by
opportunistic pathogens)

Antibiotic treatment for primary pathogen (imbalance of normal

microbiota)  opportunistic pathogens)
Stages of pathogenesis
Exposure: encounter with a potential pathogen, require a portal of entry (e.g.,
mucosal surfaces, breaks in skin)
Adhesion: pathogens attached to cells of the body
Invasion: dissemination of a pathogen throughout local tissues or the body
Infection: led by the successful multiplication of the pathogen
What determines the pathogenicity of a
microbe?
Must be able to colonise mucosal surfaces (adhere, compete for
nutrients, multiply) and resist host defences

Pathogens express Virulence Factors (VF) that help them to survive

or grow in the host
VFs determine the extent and severity of disease they may cause
VFs encoded on a plasmid or phage that can transfer horizontally
between microbes are called pathogenicity islands  make non-
invasive species become pathogenic
Virulence Factors
Attachment:
- Adhesin

Invasion:
- Exoenzyme (extracellular enzyme)
- Toxins

Secretion systems that help secrete exotoxins

Capsule to prevent immune detection
Adhesin
A protein or glycoprotein found on the surface of a
pathogen that attaches to receptors on the host cell
Pilus (pili, hair-like, in some G- bacteria)
Fimbria (fimbriae, in both G- and G+ bacteria)

Nonpilus adhesins (bacterial surface protein) 

tighten interactions between bacteria and host cells
Biofilms (organized, high-density of cells)  persistent
adherence and resistance to host defense and
antimicrobial agents
Exoenzymes (extracellular enzyme)
Enable pathogen invade host cells and deeper tissues (e.g. hyaluronidase
produced by Staphylococcus aureus)

透明质酸

A portal of entry
Toxins
Assist pathogen to invade host cell and cause damage to tissues
Toxigenicity: a pathogen’s ability to produce toxins to cause damage to host cells

Classification:
◦ Endotoxin: Lipopolysaccharide (LPS) in G- bacteria and cause hyperactivation
of immune system via Toll-like Receptors (TLRs)
◦ Exotoxin: secreted protein toxins that disrupt host’s cellular processes or
immune response (mycotoxin in fungi)
◦ Endotoxin is released only when the bacteria is killed, whereas, exotoxins are
produced by living bacteria.
Endotoxin/Lipopolysaccharide (LPS)
Found on the outer membrane of G- bacteria
Consists of
◦ Lipid A (=lipo) relatively conserved  responsible for LPS toxigenicity 
trigger the inflammatory response of immune system
◦ Core oligosaccharide
◦ Putative O-antigen (long polysaccharide)
Endotoxin/LPS
Stimulates TLR4 (a transmembrane protein of
PRR families)
◦ Downstream signaling cascade
◦ Leading to pro-inflammatory stimulus
◦ Can give rise to septic shock during
bacteremia

 Bruce Beutler was awarded a portion of the

2011 Nobel Prize in Physiology or Medicine
for his work demonstrating that TLR4 is the
LPS receptor
Exotoxin
Produced primarily by G+ bacterial pathogens (living)

Interact specifically with host cell

Example: diphtheria toxin 白喉毒素, produced by Corynebacterium

diphtheria  inhibit protein synthesis in host cell  cause
cutaneous diphtheria 皮肤白喉
Differences between endotoxin and
exotoxins
Capsule
Attached tightly to the bacterium (up to 10 µm thick)
Consisted of polysaccharides or proteins

Functions:
Not essential for viability (capsular polysaccharides removed enzymatically
from cell surface)
Contain water which protects the bacteria against desiccation
Protect a bacterial cell from ingestion and destruction by white blood cells
(phagocytosis)
Host defence mechanisms
First line of defence:
◦ physical barriers
◦ Skin (dry, salty and acidic, credited to fatty acid), wound
◦ Mucous membranes (mucus layer, antimicrobial peptides) Entry deny
◦ Blood-brain barrier (endothelia, central nervous systems)
◦ others
◦ Cilia in airway
◦ Enzymes in tears and saliva Pathogen
Killing/Removal
◦ Acid in stomach
◦ Resident microbiome (binning site and nutrients) Niche/resources completing
Second line of defence: immune system
Immune system
Innate immunity: immediate (non-specific) response to pathogens
◦ Recognizes Pathogen Associated Molecular Patterns (PAMPs) like LPS,
peptidoglycan, surface proteins
◦ Involves receptors like
◦ TLRs
◦ C-type lectin receptors (CLRs)
◦ NOD-like receptors (NLRs)
Adaptive/acquired immunity: specific response
◦ antibodies (humoral)
◦ white blood cells (cell-mediated)
Development of diseases caused by
microbes
Host defence mechanisms tend to Microbes gain access to the host,
antagonize the actions of invading adhering to and colonizing cell surfaces,
micro-organisms. invading tissues, and producing toxins
and other harmful metabolic products.

The occurrence of a disease depends on whether the pathogen or the host

defence mechanism wins the battle.
The Etiology of Infectious Diseases
Learning objectives
Etiology of a disease = why does the disease occur?

Classification of diseases

Spread of diseases

How to trace the pathogen of an infectious disease

40
Symptoms, Signs and Syndrome
Symptoms: changes of body functions; subjective,
inapparent to observers, cannot be
clinically confirmed or objectively measured
(e.g. stomach ache)
http://media01.money4invest.com/2010/03/h1n1-flu-like-symptoms.jpg

Signs: objective changes that can be measured (e.g. body temperature, blood
pressure, presence of antibodies)

Syndrome: a specific group of signs and symptoms characteristics of a particular

disease
Diagnosis
Diagnosis: symptoms + signs + lab tests

Complicated by the fact that different microorganisms can cause similar

signs and symptoms in a patient.
◦ e.g. many bacterial (e.g., Listeria monocytogenes) and viral pathogens
(rotavirus) associated with diarrheal disease

Asymptomatic or subclinical disease (no noticeable signs or symptoms).

◦ Coronavirus remain asymptomatic in individuals (infection unaware)
Two aspects of a disease’s morbidity
Prevalence: the proportion of all
cases (existing and new) of a
disease at a given time

Incidence: the frequency of new

diagnosed cases of a disease in a
population during a certain period
of time
Classification of diseases (1):
infectiousness
Communicable (e.g. tuberculosis)
- Spread from person to person directly/indirectly

Mycobacterium tuberculosis

Non-communicable (e.g. Tetanus caused by

Clostridium tetani)

Clostridium tetani
Classification of diseases (2): occurrence
Sporadic: occur occasionally, without geographic concentration (e.g. tetanus)

Endemic: constantly present (often at low level) in a population or region (e.g.

Malaria in some regions of Brazil)

Epidemic: an outbreak of a disease in a short time within a geographic region

(e.g. Influenza occurs during winter)

Pandemic: occur worldwide (e.g. Covid-19, HIV)

Classification of diseases (3): Severity or
duration
Acute: develops rapidly but lasts for short time
(e.g. flu)

Chronic: develops slowly, but can last long time

(e.g. Mycobacterium tuberculosis granulomas,
or Candida albicans in genital tract)

Latent: e.g. Rickettsia prowazekii (causes Typhus

斑疹伤寒症) can go into latent phase for up to
years without active replication
Spread of communicable diseases
Reservoirs of infections

Transmission of diseases

Nosocomial infections
Reservoirs of infections
 Human (latent or active)
- passive carrier: contaminated with the pathogen and can mechanically
transmit it to another host, but not infected.
- active carrier: an infected individual who can transmit the disease to others,
but may not exhibit signs or symptoms of infection (asymptomatic carriers)

 Animals (zoonotic diseases, H5N1 influenza a.k.a. bird flu)

 Arthropodic vectors (e.g. mosquitos, ticks)
 Nonliving reservoirs: contaminated water (Vibrio cholerae), soil where animal
feces are used as fertilizer, contaminated food
Transmission of infection
Person-to-person transmission:
 Direct through body fluids (blood, saliva, semen)
◦ Sexually transmitted infections (HIV, syphilis, gonorrhea and genital herpes)
◦ Blood transfusions
◦ kiss
 Direct through droplet (coughing, sneezing)
 Indirect through fomites (contaminated inanimate objects, towel)
 Indirect through contaminated syringes (drug userstransmission of HIV)
 Vertical direct transmission from mother to baby
Transmission of infection
Vectors
◦ Inset/mammals/birds (dogs/bats rabies virus; cattle Bacillus anthracis
(anthrax)
◦ Arthropods (ticks  Lyme disease)

 Vehicles (non-living)
◦ Water (poor sanitation)  waterborne transmission
◦ Food (poor handing or storage)  foodborne transmission
◦ Air (spores from fungi, hanavirus) airborne transmission
Nosocomial (healthcare-associated)
Infection
Hospital-acquired infection or HAI (>5% of all admitted patients in developed
countries)

Microbes (opportunists, resistant to antibiotics)

Immuno-compromised host

Control of nosocomial infection: hand washing, and other disinfection methods

Key pathogens of nosocomial infections
Bacteria
Staphylococcus aureus, particularly those resistant to methicillin (MRSA)
Escherichia coli
Pseudomonas aeruginosa
Enterococci
Clostridium difficile
Virus
Norovirus
Respiratory Syncytial Virus and Influenza
Fungi
Candida species
Summary
Types of symbiosis

From pathogen to disease

Virulence Factors

Host’s defense system

Classification of diseases

Infectious diseases

Reservoirs of diseases

Transmission of infection