Bacterial Genetics

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 Definitions
The gene
• The basic unit of inheritance formed of a segment of DNA
molecule that carries in its sequence the information for specific
biochemical or physiological function.
• Genes are located on the chromosome.
The genome
• The entire collection of hereditary material (DNA) within a cell ,
it includes chromosomal and extra-chromosomal DNA
(Plasmids).
The genotype
• A set of genetic (heritable) determinants within the cell.
The phenotype
• The observed properties exhibited by the microorganisms under
the influence of the environment.

Structural classification of genetic elements of

bacterial cells
1- Bacterial chromosome

 It is an organized structure of DNA inside the cell.

 Chromosomal DNA is coiled and contain many genes, regulatory
elements and other nucleotide sequences.
 Bacteria have only one circular chromosome (the nucleoid region),
Thus bacteria are considered haploid.
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2- Plasmids

 Extrachromosomal double stranded DNA that replicates independently of

the bacterial chromosome.
 They are usually circular and maintained in the supercoiled configuration
in order to save place.
 They vary in size from one to hundreds of kilobases.
 Bacterial cells may contain numerous plasmids which may be of the same
type or different types.

 Episomes → Plasmids able to integrate into the host chromosome.

• Genes encoded by the plasmids •

1- Genes necessary for their replication → Origin of replication genes (Ori
gene).
2- Genes necessary for transfer via conjugation → (tra gene)
3- Genes coding for specific function
I. Physiological function → nitrogen fixation.
II. Antibiotic production
III. Antibiotic resistance → R-Factors.
IV. Virulence determinants as gene of neurotoxin production by Cl.
Tetani
V. Production of Bacteriocins as Colicins produced by E. coli are
controlled by plasmids which are called Col factors.
Bacteriocins are bacterial substances produced by certain
strains of bacteria against some other strains of the same or
closely related species
VI. Fertility factor → can mediate gene transfer by conjugation.

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3- Transposable genetic elements

Definition
Mobile sequences of genes that can move (transpose) into different sites
in the microbial DNA (Chromosome or plasmid), so it is called “Jumping
genes”.

Classes of transposable genetic elements

a- Insertion sequences
about 1000 bps in size bounded by inverted and direct repeats.
b- Composite transposons code for →
• Their own replication
• insertion
• transposase enzyme which enables them to recombine with
bacterial DNA by themselves.
c- Conjugative transposons
incorporate additional genes within their structure as antibiotic
resistant genes.

Importance of transposable genetic

elements
Coding and the inter-bacterial transfer of virulence genes in the form
of pathogenecity associated islands (PAIs)
PAIs → special class of mobile genetic elements containing groups of
virulence genes which are absent in non-pathogenic bacteria ….
Examples :
1- Uropathogenic E. coli
(hemolysins and pili)
2- Helicobactor pylori
3- Vibrio cholera

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 The Genetic variability of bacteria
“Bacterial Variation”

Changes in the genome can occur by 2 processes

1- Mutation

Definition → A permanent change in the DNA sequence.

 As bacteria are haploid and clonal (divides by binary fission), variations
resulting from mutation rearrangement will be passed from one parent to
daughter cells and such transfer is termed vertical.
Causes
a- Spontaneous Mutation
Natural mutation that happens without the presence of a mutagen.
b- Induced mutation
By mutagenic factors “Radioactivity & UV rays & alkylating-chemicals”

2- Intracellular Gene Transfer

Mechanisms which involve a unilateral transfer of genetic information from a

donor cell to a recipient cell are called “Parasexuality”
The transferred DNA either :
i- Recombines with the genome of the recipient cell or
ii- Remains as a plasmid capable of replication in the recipient without
recombination.

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 A- Transformation

 The uptake of fragments of free naked DNA from the environment and
subsequent recombination into the new recipient cell.
 However, nucleases secreted from most cells will quickly degrade free DNA
and prevent widespread transfer of genes.

B- Transduction

 it is the transfer of DNA from a donor to a recipient with the help of

transport bacteriophage.
 Bacteriophage are viruses that infect bacteria, during their replication
process, DNA, sequences from the host bacterial cell may replace all or part
of the genome in the phage head.

Types “depend on the type of lifecycle of different phages”

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 1-Specialized transduction

 it is the transfer of specific parts of bacterial DNA with a phage DNA to

another bacterial cell.
 It occurs when the phage entering the bacteria undergoes a Lysogenic cycle
“temperate phage”

Lysogenic Life cycle “temperate cycle”

i- The phage enters the bacterial cell.

ii- Attaches its genome at specific sites of the bacterial genome (site-
specific insertion).
iii- The phage remains viable (prophage) but is dormant (repressed).
iv- Upon activation (by UV rays) → the prophage excises itself and
takes some segments of the bacterial genes adjacent to the
excision sites.
v- The activated phage then causes lysis of the bacterium.
vi- Infect the next bacterial host.

2-Generalized Transduction

 transfer of any bacterial gene to another bacterium through a

bacteriophage.
 Generalized transduction occurs when the phage entering the bacterial host
undergoes a Lytic cycle (Virulent phage)

Lytic cycle of phage

i- Phage genome enters the bacteria but does not attach

itself in the bacterial genome (it exists autonomously to
bacterial chromosome).
ii- The phage replicates its genetic material and packs it into
its own capsule.
iii- During the packing process → random fragments of the
bacterial DNA are incorporated into the phage capsule
iv- The bacterial cell is lysed to allow exit of the phage which
can infect another host. Page | 7
 C- Conjugation

Transfer of DNA from a donor to a recipient after cell-to-cell contact.

1- Conjugative plasmids characters (F Plasmids)

a- High frequency of transfer → each receptor cell that has received a
conjugative plasmid automatically become a donor cell ( F+ )
b- Wide range of hosts → many conjugative plasmids can be
transferred between different taxonomics (species & genera &
families)
c- Multiple determinants → many conjugative plasmids carry several
genes determining the phenotype of the carrier cells.

2- Conjugative transposons
 DNA elements that are usually integrated into the bacterial
chromosome
 It may carry determinants for antibiotic resistance and this
contribute to horizontal resistance transfer. Page | 8
 Conjugation Process

a- The bacteria produce sex pili → attach the donor & recipient and
draw them together.

b- The pilus retracts → a single strand of the F Plasmid is

transferred through the pilus to the recipient.

c- Separation of the mating pair

d- Complementary second strand of the plasmid is then synthesized
by the recipient

Plasmid replicates → 2 copies → one for

D- Transposition

The process by which insertion sequences or transposons can be

transferred among bacteria.

Mechanism

1- Simple transposition → the transposon is excised from the donor and

inserted into the recipient (Cut and paste mechanism)

2- Replicative transposition → the transposon replicates to make a copy in the

donor and then the copy is transferred to the recipient (Copy and paste
mechanism)

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 The host-parasite relationship can be viewed as a series of stages that
begins with contact, progresses to infection and ends in disease.
Because of numerous factors relating to host resistance and degree of
pathogenicity, not all contacts lead to infection, and not all infection
lead to disease.

Colonization

The presence of micro-organisms, pathogenic or non-pathogenic, in large

numbers, on a host without tissue damage or clinical disease.

Infection AND Disease

Infection is the process by which the parasite enters into a relationship

with the host.
Disease is the destruction of host tissues by the organisms due to
invasion of tissues, toxin production or other virulence factors.

It requires the following:

a. A source of infection which may be man (case or carrier), animal or soil.
b. Mode of transmission → insects bite, fecal contamination of food, inhalation of
droplets, sexual contact, blood transfusion or transplacental.
c. A portal of entry into the host → gastrointestinal, genitourinary, respiratory
tracts, skin and mucous membranes and through abrasions, insect bites or
injections.
d. Multiplication of the parasite within the host → the parasite may multiply locally
at the portal of entry or it may spread through the tissues, blood or lymphatics to
reach a target organ.
e. Portal of exit from the host → in urine, stools, respiratory, genital discharges or
from the blood by insects or injections from which the organism will be
transmitted to another host.

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Carriers:
 They are apparently healthy individuals carrying a pathogenic organism without
showing clinical manifestations.
 They can transmit this organism to other susceptible individuals.
 Carriers can be transient carriers (during the incubation period) or permanent
(chronic) carriers as in hepatitis B.

 The site of carriage may be:

1. Intestinal or urinary salmonella carriers which cause enteric fever.
2. Nasopharyngeal carriers causing epidemic cerebrospinal meningitis.
3. Throat (oropharyngeal) carriers causing diphtheria.
4. Nasal, skin or throat carriers causing staphylococcal infections.
5. Blood carriers causing hepatitis B and C and HIV infections.

 Carriers are more serious than cases as a source of infection because:

1. They are not confined to bed.
2. They do not show manifestations of the disease.
3. They communicate with the public without being noticed.
4. They carry the organism in the inter-epidemic period.

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 TYPES OF PATHOGENS

pathogens: are microorganisms which are capable of causing disease .

Two main types of pathogens

1- True pathogens:

those who are capable of causing disease in healthy persons.

2- Opportunistic pathogen :

• are those that rarely cause disease in immune-competent people but can
cause serious infections in immune-compromised patients.
• These opportunists are frequently members of the body's normal flora.

• Under certain conditions, commensal bacteria may cause disease :

1- Lowered host defense mechanisms → immunosuppressed, diabetes,
leukemia
2- Alteration of the host tissue → viridans streptococci is a normal flora in
mouth and throat but may reach the blood stream and cause
endocarditis after tooth extraction is the host has a heart lesion
3- Change in the natural habitat of the organisms → E. coli is a normal flora
of intestine .. if it reaches the renal system it causes urinary tract
infections.

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 TYPES OF INFECTIONS

According to the distribution

1. Endemic infection: which is constantly present at a low level in a specific
population.
2. Epidemic infection: The infection that occurs much more frequently than
usual.
3. Pandemic infection: if it has a worldwide distribution

According to the extent of spread

1. Localized infection: the infection that occurs at the portal of entry.
2. Systemic infection: the infection that spreads to several sites tissue fluids.

According to the sequence of infection

1. Primary infection: the initial infection caused by the organism.
2. Secondary Infection: occurs if the initial infection is complicated by other
infection caused by a different microbe.

According to the progress of the infection

1. Acute infections: are those that arise quickly (tonsillitis) and progress
rapidly.
2. Latent Infections: are those in which the microbe is able to persist for years
within a site in the host and cause minimal clinical disease for most of the
time the organism is present.
3. Chronic Infection, in which the organisms continue to grow with or without
producing symptoms in the host. Chronic carriers are an important source of
infection and hence are a public health hazard.

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 CLASSICAL STAGES OF CLINICAL INFECTIONS

1-The Incubation period: the time from initial contacts with the infectious
agents to the appearance of the first symptoms.

2-The Prodromal stage: The earliest symptoms of infection appear as a vague

feeling of discomfort, generalized body ache.

3-Period of invasion: The specific signs and symptoms exhibited by the patients
according to the site of infection.

4-Convalescent period: The period of recovery.

STAGES OF BACTERIAL PATHOGENESIS

1- Transmission from an external source into the portal of entry.
2- Evasion of primary host defenses such as skin or stomach acid.
3- Adherence to mucous membranes, usually by bacterial pili.
4- Colonization by growth of the bacteria at the site of adherence.
5- Disease symptoms caused by toxin production or invasion accompanied by
inflammation.
6- Host responses, both nonspecific and specific (immunity) during steps 3,4,5.
7- Progression or resolution of the disease.

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FACTORS THAT GOVERN DISEASE PRODUCTION
• Only few infections end in clinically manifested disease.
• Most infections are abortive, silent or subclinical.
The outcome of infection depends on interactions between:
1- Host resistance factors (natural and acquired immunity).
1- Microbial factors (pathogenicity and virulence).

1- Host factors:
A- innate immunity → mechanical barriers, chemical barriers, and innate cell
(macrophage, dendritic cells).
B- acquired immunity antibodies and T cells.

2- Microbial factors

Pathogenicity: is the ability of an organism to cause disease.

Infectious dose:
• The dose of organism required to cause disease.
• disease varies greatly among the pathogenic bacteria.
• For example, Shigella and Salmonella both cause diarrhea
infectious dose of Shigella is less than 100 organisms
infectious dose of Salmonella is on the order of 100,000 organisms.

Virulence:
• is a quantitative measure of pathogenicity “degree of pathogenicity”
• measured by the number of organisms required to cause disease

Virulence Factors:
 these are certain structures or products that help microorganisms to
overcome body defense mechanisms and cause disease.
 expression of virulence genes is regulated by several genetic, nutritional
and environmental factors as availability of nutrition (iron – oxygen –
suitable temperature).
 Virulence genes can move between bacterial via special genetic vehicles →
plasmids, bacteriophages and transposons.

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 1. Transmissibility
• The first step of the infectious process is the entry of the microorganism into
the host.
• Once entry is achieved, the pathogen must overcome a diversity of host
defenses
• Bacteria that have an outer polysaccharide capsule for example,
Streptococcus pneumoniae, and Neisseria meningitidis have a better chance
of surviving the host defenses.

2. Adherence to host cells

• Mediated in some bacteria by Pili (E.Coli).
• Adherence enhances virulence by preventing the bacteria from being carried
away from organs with significant fluid flow such as the urinary tract and the
gastrointestinal tract.

3. Invasiveness
invasive bacteria are those that can enter host cells or penetrate mucosal
surfaces, thereby spreading from the initial site of infection.

A- Enzymes → collagenase and hyaluronidase, These enzymes degrade

components of the extracellular matrix, thereby providing the bacteria with
easier access to host cell surfaces.
B- Invasins → specific bacterial surface proteins help entry into cells.

Invasion is followed by inflammation depending on the organism

a- Pyogenic (pus formation contain mainly neutrophils)
b- Granulomatous (nodular lesions contain fibroblasts, lymphocytes,
macrophages)

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 4- Bacterial toxins

Endotoxin Exotoxin
1- TYPE OF BACTERIA Gram -ve Gram +ve & -ve
2- CHEMICAL NATURE Lipopolysaccharide Protein
(10 KDa) (50-1000 KDa)
3- COMPONENTS a- Poly saccharide O 2 polypeptide
b- A core of components
polysaccharide • 1st for binding to the
host
c- Lipid A
• 2nd for the toxic
effect
4- RELEASE After cell lysis Secreted
5- RELEATIONSHIP IN Parts of outer Extracellular
CELL membrane
6- DENATURATED BY NO YES
BOILING
7- IMMUNOGENICITY Weakly Highly
8- FORM TOXOID No Yes
9- POTENCY Low ( >100µg) High( 1 µg)
10- PYROGENICITY Yes Occasionally

11- SPECIFICITY Low degree High degree

12- ENZYMATIC No Usually
ACTIVITY
13- EFFECTS Septic shock Tetanus

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 5- Enzymes
(1) Collagenase and hyaluronidase

• degrade collagen and hyaluronic acid → spread through subcutaneous

tissues
• they are especially important in cellulitis caused by Streptococcus
pyogenes.

(2) Coagulase
• produced by Staphylococcus aureus
• accelerates the formation of fibrin clot from its precursor fibrinogen (this
clot may protect the bacteria from phagocytosis by walling off the
infected area and by coating the organisms with a layer of fibrin).

(3) Immunoglobulin A (IgA) protease

which degrades IgA, allowing the organism to adhere to mucous
membranes
produced chiefly by Neisseria gonorrhoeae, Hemophilus influenzae, and
Streptococcus pneumoniae.

(4) Leukocidins
which can destroy both neutrophilic leukocytes and macrophages.

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