C1bT1L16

Introduction to Medical Microbiology

Burt Anderson, Ph.D.

1
 Objectives
Supplemental Reading: Sherris Medical Microbiology, 7Ed,
appropriate sections of chapters 1, 5, 16, 17 and 21. Bug
Bios

• Describe bacteria, viruses, eukaryotic pathogens.

• Recognize the basic properties of each of the
different microbe groups (prions, viruses, bacteria,
fungi, protozoa and helminths) that cause human
disease.
• Explain mode of transmission.
• Contrast primary vs. opportunistic infections.
2
 Why is microbiology important?

• Emerging infectious diseases

– Old diseases in new places
– New association of old microbes
with disease
– Newly described pathogens
• Microbes resistant to treatment
• Intentional release of microbes
(bioterrorism)
• http://www.cdc.gov/ncidod/EID/
3
Why is microbiology important?

4
 Types of microbes
• Commensal: normal flora, part of the
microbiome, not associated with disease
• Opportunist: may be normal flora,
associated with disease under certain
conditions (immunosuppression,
relocation)
• Pathogen: associated with human
disease, primary infection
5
 Bacteriology - terms
• Commensal – microbes that are permanent residents
of a given non-sterile body site (i.e. normal flora,
microflora)
• Pathogen – microbe that is capable of causing disease
• Opportunistic pathogens – usually do not cause
disease in healthy immunocompetent individuals but
can cause disease in immunocompromised individuals
or individuals with other risk factors (trauma, burns,
AIDS, genetic predisposition)
– Pseudomonas aeruginosa
 Microbiome -terms
• Microbiome - The ecological community that
shares our body
• Microbiota – the microbes comprising the
microbiome (i. e., microflora)
– Bacteria
– Bacteriophages
– Viruses
– Fungi/yeasts
• Dysbiosis – alteration of the relative abundance of
all or part of the microbiota
 Meet the “Bugs”
• Prions
• Viruses
• Bacteria (prokaryotic)
• Fungi (eukaryotic)
• Protozoa (eukaryotic)
• Helminths (worms, eukaryotic)
• Ectoparasites

8
9
 Viruses vs Bacteria
• Bacterium
Virus
– Larger
Smaller
– Free
Non living
living
– Cell
Replicate
division
– Most
Requiredo host
not require
cell for:host cell for basic
functions
• Macromolecular synthesis
• Assembly of progeny
• replication

10
 Prions

• Cause “transmissible” spongiform

encephalopathy
• proteins
• Facilitates misfolding of cellular proteins
PrPC PrPSC
• Does not replicate
• Endogenous form must be present in host
• Neurotropic

11
 Viruses
Components of a basic virion

12
 Fungi

• Eukaryotic
• Cells larger than bacteria
• External rigid cell wall (chitin)
• Two forms; yeast, mold
• Free-living
• Most cause opportunistic infections

13
 Protozoa

• Single cell
organisms
• Eukaryotic
• May have different
forms (e.g. cysts,
sporozoites)
• May have an
alternate host or
vector
14
 Helminthes

• Eukaryotic
• Many worms are highly
differentiated with organ
systems
• Most worms have
complex life cycle
involving several stages
and intermediate host
• Some tapeworms > 1
meter in length

15
 Case 1
• A man awoke to let his dog into his fenced
back yard. He heard a commotion and
saw his dog fighting with a racoon. In
separating the two animals he sustained
scratches and a possible bite from the
racoon.
 Lab Testing Case 1
• The racoon was captured, euthanized and
the brain tissue was tested for the
suspected pathogen using a specific
fluorescent labeled antibody

Racoon brain tissue Negative control brain

Electron Microscopy of the Suspected
Agent in Cases 1
 Based on the microbiological properties of the
suspected etiologic agent, which one of the following is
the most accurate description?

1. Prion No, affects CNS but does not have morphology

observed by electron microscopy
2. Virus YES, visible only by electron microscopy with bullet
shaped virion
3. Bacterium No, would by visible by light microscopy and
be much larger
4. Protozoa No, much larger and visible by light microscopy
5. Helminth No, most likely multicellular and larger

20
 Case 1
• The potentially exposed individual received
post-exposure prophylaxis for rabies
• Rabies ~ 100% fatal if untreated but
~100% survival with post-exposure
treatment
• Valrico, FL, January 2020

http://hillsborough.floridahealth.gov/newsroo
m/2020/01/rabies-valrico.html
Modes of transmission
1. Respiratory/ aerosols

• Influenza
• Tuberculosis
• COVID-19
Transmission of respiratory pathogens
– AEROSOLS!

23
Modes of transmission
2. Fecal-oral

• Escherichia coli
• Norwalk virus
Modes of transmission
3. Sexual

• Gonorrhea
• Herpes virus
Modes of transmission
4. Arthropod-borne

• Zika virus
• Malaria
Modes of transmission
5. Zoonotic with animal reservoir

• Rabies
 Modes of transmission
6. Zoonotic with animal reservoir and arthropod vector

• Lyme disease
• Plague
 Entry Portals/Exposure

• Portals of entry • Ingestion

– Skin, eyes, ears • Inhalation
– Respiratory tract • Trauma
(nasopharynx)
– Gastrointestinal Tract
• Needle stick
(mouth) • Arthropod Bite
– Urogenital tract • Animal bite
– Trauma (anywhere) • Sexual transmission
Prokaryotes vs Eukaryotes

30
A Bacterial Cell

31
 Bacterial Structures
• nucleoid - no nuclear membrane, one
chromosome, 1-5 million base pairs
• plasmids - replicate independently of
chromosome, often code for virulence
factors or antibiotic resistance genes
• cytosol - no organelles except ribosomes
• ribosomes - site of protein synthesis, two
subunits
32
 Bacterial Taxonomy

• classic Linnean (binomial) nomenclature,

genus and species with some descriptive
information
Staphylococcus aureus
Streptococcus pneumoniae
Haemophilus influenzae
Escherichia coli

33
 Cell shapes of bacteria

coccus

bacillus

spirochete

34
The “Big Four” typical bacteria (Fig.
10-2)

35
The Gram Stain Reaction

36
 Study Points/Questions
• What are some of the fundamental differences between:
– Prokaryotic and eukaryotic cells
– Bacteria and viruses
– Prions and all other microbes
– Fungi and protozoa
• What are the steps of the Gram stain and how does it help
identify bacteria?
• What are the different modes of transmission and portals of
entry for microbes?
• What is the difference between commensal, opportunistic and
pathogenic microbes? Is there any overlap between these
designations?

37
 Bug Bio: Zika Virus
 Pathogen: Zika Virus

 Physical and structural description

 Flavivirus
 Genome is positive-sense RNA
 Origin/Reservoir, Transmission, Epidemiology
 Humans and monkeys are hosts
 Transmitted by mosquito bites, sexual transmission, blood
transfusion, during pregnancy
 Disease
 Zika fever, AKA Zika virus disease
 Fever, rash, red eyes, joint pain
 Infection during pregnancy associated with microcephaly
 In adults linked with Guillain-Barre syndrome
 Congenital Zika Virus Syndrome
 Microcephaly
 Pathogenesis/Virulence
 Viral replication near site of infection
 In fibroblasts, dendritic cells
 Spread to lymph node and blood
 Diagnosis
 Blood, urine or saliva may be tested for viral RNA
 Serum tested for IgM to Zika virus by ELISA
 
 Treatment/Prevention
 Currently no effective specific treatment
 No approved vaccine
 Prevention by mosquito control and safe sex/abstinence after
possible exposure 38
 Adhere to travel warnings
 
 Bug Bio: Rabies Virus
 Pathogen: Rabies Virus

 Physical and structural description

 Rhabdovirus
 Genome is negative-sense RNA
 Bullet-shaped, enveloped virion
 Origin/Reservoir, Transmission, Epidemiology
 Wild animals (raccoons, bats) are hosts
 Transmitted by animal bite, rarely by aerosols
 Disease
 Rabies (encephalitis)
 Prodrome of fever, anorexia, paresthesias
 Agitation, delirium, seizures, photophobia
 Survival is very rare in untreated
 Pathogenesis/Virulence
 Viral replication near site of infection (bite)
 Virus attaches to acetylcholine receptor
 Axonal transport of virus to CNS
 Replication in the brain
 Virus migrates to salivary glands
 Diagnosis
 Testing of animal brains by direct fluorescent antibody staining,
immunostaining or PCR
 Stains for inclusions (Negri bodfies) in brain tissue of animals
 
 Treatment/Prevention
 Currently no specific anti-viral treatment
 Pre-exposure vaccine
 Post-exposure treatment includes passive immunization with rabies
immune globulin and vaccination is very effective 39
 Canine immunization prevents rabies in dogs
 
 Bug Bio: Coronavirus – SARS-CoV-2

 Pathogen: Coronavirus
 Physical and structural description
 Enveloped virus with helical nucleocapsid - single piece of single-stranded, positive
polarity RNA. No virion polymerase. There are genetic variants
 Origin/Reservoir: Possibly from animal origin, initially described in Wuhan, China in
late 2019
 Transmission human to human transmission occurs via air-borne respiratory droplets

Disease
- COVID-19 symptoms appear in 2-14 days and may include:
- Fever or chills
- Cough, sore throat, congestion or runny nose
- Shortness of breath or difficulty breathing
- Fatigue
- Muscle or body aches, headaches
- New loss of taste or smell
- Nausea or vomiting
- Diarrhea
• Diagnosis
• PCR assay detecting viral RNA in respiratory tract specimens (swabs, saliva).
• Antigen detection and antibody-based tests are also available.

 Treatment/Prevention
 Experimental use authorization (EUA) for antiviral (Remdesivir), monocloncal antibodies
and convalescent plasma No specific antiviral therapy
 EUA from CDC/FDA for RNA-based vaccines (Pfizer, Moderna) and recombinant
adenovirus vectored vaccine (J & J/Janssen) encoding portions of spike protein