Pathogenesis of bacterial infections
11 August 2020 14:03
Bacterial taxonomy/ Pseudomonadaceae
Understanding taxonomy and phylogeny (classification and evolution of bacterial species)
Topic 1: Taxonomy and phylogeny: Bacteria and Archaea
Bacteria and Archaea are two different single groups of organisms.
Definitions
Taxonomy: Classification based on the shared characteristics (phenetic, overall similarity).
Phylogeny: Measures the evolutionary relationships between organisms.
Classification of bacteria:
Traditional properties used in classification:
- Microscopy/ Morphology
- Response to oxygen
- Mode of energy synthesis/ source of carbon
- Biochemical, enzymatic tests
Molecular and genetic methods:
- Choose appropriate molecular markers for a gene family
- Amplify and sequence
- Create evolutionary model
- Phylogenetic tree analysis and construction
All living organisms have genes which mature randomly (base changes) at low frequency.
All progeny (offspring) will carry the mutation (base changes)
Organisms differing by a few DNA base changes have diverged more recently in evolutionary time than organisms that
differ by more bases.
Steps in taxonomic classification of microbes:
Carl Linnaeus (founder of modern taxonomy 1708-1778)
He is the first to originate the seven of the kingdoms, phylum and so on down to species.
1) Classification:
Ordering organisms into groups, based on shared properties.
2) Nomenclature:
Naming the classified organisms
3) Identification:
Obtaining data on the properties of an unknown organism and determining which species it belongs to, based on direct
comparison to known groups.
The taxonomic characteristics are generally changing throughout evolution but its specifically changing for bacteria
because of how difficult it is to assess their shared characteristics given that they're microscopic. There is another main
method used to classify organisms to species level, which is whether or not they can inter breed.
This is if two animals can't produce any young, they're generally regarded as different species or if they can't produce
fertile young, that's generally considered to be different species. But that’s incredibly difficult to make sure of with
bacteria because we are dealing with plasmids of organisms that would normally reproduce asexually.
So, Carl Linnaeus regarded classification of the microbial world as chaos because you simply couldn't apply the same rule
as you can to multicellular organisms.
For a long period of time there was only crude differences in morphology. For example, based on very simple light
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,For a long period of time there was only crude differences in morphology. For example, based on very simple light
microscopes or early versions of light microscopes.
In addition to staining and varying microbes, there are range of tests which can be used to categorise microbes whether
it's to do with appearance, morphology, atmospheric condition for growth or any other kinds of nutrition or enzyme
production enables nutrient utilisation.
There are molecular and genetic methods which allow to characterise microbes. For example, there are molecular
markers for a particular sequence of genes and which allows you to amplify sequences, work out the distant and common
ancestors from which current species separated.
The basis of phylogenetic relationships is that they rely on the principle called molecular clocks. Using the number of base
pairs difference you can work out how much of difference and similarities each species have as they evolved.
Internal nodes- which represent an extinct ancestor from which two species have separated.
External nodes- which represent the existing strains of species.
Formally, bacteria are named under archaea. Carl Woese (July 15, 1928- December 20, 2012) defined that archaea as
separate domain of life in 1977 by phylogenetic taxonomy of 16s ribosomal RNA. Carl Woese realised through more
modern genetic analyst that how we were regarding bacteria was actually incorrect because there were actually a
separate category called the archaea, which were very distinct and completely different branch of that phylogenetic tree.
The system had all these single cell prokaryotes as monera and eukaryotes as protists. The monera are known to be
separate and they constitute the bacteria and the archaea which is more closely related to eukaryotes. Archaea are more
closely related to eukaryotes than bacteria because of the distance between the splitting away from those internal nodes
where a common ancestor was shared.
Phylogenetic tree of major lineages of bacteria based on 16s rRNA:
The gram positives (including mycoplasmas):
(i) High Guanine + Cytosine (Actinomycetes, Mycobacteria etc.)
(ii) Low Guanine + Cytosine (Bacillus, clostridia etc.)
Proteobacteria:
A very successful group with most of the common gram negatives.
Alpha: Rhizobium, Agrobacterium, mitochondria
Beta: Thiobacillus
Gamma: Enterobacteriaceae, pseudomonas, vibrios
Delta: Desulphovibrios, myxococcus
Epsilon: Campylobacter, Helicobacter
The microbes that infect human and cause disease and infect mammals and cause disease are in the bacterial group.
Archaea have very interesting properties and are indicative of diverse of environments around the globe. But they don’t
cause any infections in mammals.
Linnaean classification system:
Sub species/ strain classification
- Biovar: Biochemical/ physiology variant
- Morphovar: differ morphologically
- Serovar/ serotype: antigenic differences
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, - Serovar/ serotype: antigenic differences
Most gram positives such as spirochetes and proteobacteria that are important as pathogens. There are 5 main groups
branching off from the archaea. They all have properties which they can be regarded as extremophiles because they are
able to survive in environments which very few other living organisms are able to survive in. Whether it is to do with the
gaseous production in methanogens (belong to domain of archaea), grounds where fossil fuels come from often in high
methane environments.
There are hyperthermophiles (very or very low temperatures) where most organisms can't survive in.
Psychrophiles are microorganisms that are able to survive and reproduce in conditions below -15 degrees Celsius (sub-
zero).
There are acidophiles which can survive at very low pHs.
Deep under the ocean there are microbes called barophiles which are able to withstand a high amount of pressure which
most organisms wouldn’t be able to withstand.
Topic 2: Pseudomonadaceae: Pseudomonads and long lost relatives
Part A: Introduction to the pseudomonads
Most of the bacteria such as pseudomonads come from proteobacteria.
Characteristics:
Despite the broad difference of the classes and genus of the pseudomonas, there are some unifying characteristics. They
are all:
- Gram negative
- Polar flagella
- Strictly aerobic (except Zyomonas)
Many genera and species within the group including:
- Pseudomonas
- Burkholderia
- Xanthamonas
- Ratonia
- Zyomonas
- Sphingomonas
- Stenotrophomonas
Pseudomonas does not grow in anaerobic conditions and conditions where oxygen level is low.
Pseudomonas aeruginosa: Causes infections in humans
Pathogenesis: No single mechanism - multifactorial
Structural:
- Adhesins/ Pili/ Extracellular polysaccharide (EPS)/ Lipopolysaccharide (LPS) which acts as a toxin
- Capsule (evades immune cells and antibiotics)
- Pyocyanin: impairs ciliary function and stimulates inflammatory response. A siderophore (absorbs iron from our
body leading to anaemia)
Pseudomonas aeruginosa produces:
Exotoxins: Inhibit protein synthesis, tissue damage ( cause damage to the host by destroying cells or disrupting normal
cellular metabolism)
Cytotoxin: Leukocyte damage and pulmonary injury (destroy cells)
Enzymes: Elastase, protease, haemolysins. This causes variety of cell and tissue damage.
P aeruginosa' s pili interacts with the human cell to which it tries to invade. The capsule on the bacteria prevents the
bacteria being attacked by our immune system and antibiotic activity. The capsule production and the EPS production
genes are switched on in aeruginosa when it receives signal about the arrival of immune cells or antibiotics. If the
bacteria comes under immune attack, it is capable of producing EPS and capsule so it can surpass the drug or immune
response coming to attack it. The more we attack, the more it defend itself (CAN DEVELOP ANTIBIOTIC RESISTANCE).
Pyocyanin is a toxin produced by aeruginosa and it has a green colour believed to be 'false copper' thinking that copper
produces the same colour over time. Pyocyanin is one of the many toxins produced and secreted by the Gram negative
bacterium Pseudomonas aeruginosa.
P aeruginosa infections in human:
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, P aeruginosa infections in human:
It is an opportunistic bacteria as it exploits failing in host defences to initiate infection.
Endocarditis: Mostly heart valves of IV drug users
Respiratory infections: 80% of Cystic Fibrosis patients colonised in lungs, cats and dogs with chronic illness.
Bacteraemia and septicaemia: in immunocompromised patients (AIDS, diabetes mellitus and severe burns)
CNS infections: Meningitis and brain abscesses after invasion from contiguous structure (inner ear or paranasal sinus)
Ear infections including external otitis: a predominant bacterial pathogen in external otitis, chronic in cats and dogs.
Eye infections: causes devastating infections in the human eye.
Bone and joint infections most often seen in IV drug users and in conjunction with urinary tract or pelvic infections.
Urinary tract infections: usually hospital acquired after catheterisation.
Gastrointestinal: any part (oropharynx to rectum) in immunocompromised individuals.
Skin and soft tissue: After breakdown of integument (burns, trauma, dermatitis, high moisture conditions).
Enterobacteriaceae: The Family
Enterobacteriaceae are Gram-negative bacteria of a large family that includes Escherichia coli, Klebsiella, Salmonella, Shigella
and Yersinia pestis.
Domain Bacteria
Phylum Proteobacteria
Class Gamma proteobacteria
Order Enterobacteriales
Family Enterobacteriaceae
Enterobacteriaceae: Genetic features:
It has a huge, diverse range of bacteria organisms (single chromosomes) ranging from 0.4Mbp (e.g. Buchnera aphidicola) to 6.4
Mbp (e.g. Klebsiella oxytoca).
• Endosymbionts have small genomes compared to non-endosymbionts
• Endosymbionts have low G+C content (20-29%) compared to others (39-60%)
Endosymbiont is any organism that lives within the body or cells of another organism most often, though not always, in a
mutualistic relationship.
Non-symbionts are organisms that can exist as free-living or in host e.g. Salmonella, Escherichia.
> Approximately, half of strains sequenced contained extra chromosomal DNA in form of plasmids (58% carried between 1 -
6 plasmids). (This can benefit non-symbionts lifestyles)
When organisms like endosymbiont becomes more adapt to an environment, it G-C contents reduce (genome size shrink)
compared to those adapt to survive in multitude of environments.
Enterobacteriaceae: general morphological and biochemical characteristics:
Enterobacteriaceae is a family of:
- Gram-negative
- Facultatively anaerobic
- Non-spore-forming rods
Characteristics of this family include being:
- Motile (via peritrichous flagella) (a few exceptions)
- Catalase positive and Oxidase negative (lack cytochrome c)
- Reduction of nitrate to nitrite (few exceptions)
- Acid production from glucose fermentation (+/- gas production).
Enterobacteriaceae: natural habitats:
Gastrointestinal tract of hosts including humans, animals and insects.
Widespread contamination of environment:
○ Sewage
○ Soil
○ Water
○ Plants
○ Food
Important genera within Enterobacteriaceae:
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