Microbiology 1-8

Microbiology Textbooks

• Key microbiology textbooks include Prescott's Microbiology (8th ed.) by Willey et al., published by McGraw-Hill Higher Education; Brock Biology of Microorganisms (14th ed.) by Madigan et al., published by Pearson; Hugo & Russell's Pharmaceutical Microbiology (8th ed.) by Denyer et al., published by Blackwell; and Russell, Hugo & Ayliffe's Principles and Practice of Disinfection, Preservation and Sterilization (5th ed.) by Fraise et al., published by Wiley-Blackwell.

Learning Objectives

• Gain understanding of basic microbiology principles, including definitions of microbiology and microorganisms, and methods for studying microbes.
• Understand the importance of microbiology in areas like human health & wellbeing and pharmaceuticals/biotechnology.

What is Microbiology?

• Microbiology is the study of microorganisms (microbes).
• Microbes include bacteria, viruses, fungi, archaea, parasites, and protozoa.
• Microbiology has significant impact on various fields, such as food production, sewage treatment, agriculture, disease study, pharmaceuticals and biotechnology.

What are Microbes?

• Microorganisms (microbes) are microscopic (<1 mm) and often unicellular.
• Viruses are acellular.
• Fungi can form multicellular structures.
• Microbes are present in nearly every environment.
• The first organisms on earth.
• Greatest genetic diversity.
• Microbes outnumber human cells by a great margin.

Top causes of death in UK

• Data shows changes in top causes of death in the UK between 1915 and 2015. Infectious diseases were a more significant cause; notable declines in infectious diseases due to medicinal advances like the invention of Penicillin.

Microbes and Health

• Not all microbes are harmless. Some microbes can cause serious diseases and infections.
• Microbes play a role in non-infectious diseases, like stomach ulcers and obesity.
• Some types of bacteria can be beneficial or commensal.
• Examples of harmful bacteria include E. coli O157:H7. Examples of beneficial bacteria include E. coli Nissle 1917.

Normal Flora

• Normal flora are organisms that live in a benign symbiotic relationship with their host.
• Example of normal flora is E. coli.
• These microbes can be important in preventing infection.
• If conditions change (e.g. immune deficiency, stress, hormonal changes, environmental changes), they may overgrow and cause infections.

Challenges in Medical Microbiology

• Antibiotic resistance is a significant concern.
• Misuse of antibiotics has accelerated the development of resistance.
• Antimicrobial resistance is estimated to lead to millions of deaths per year.

Microbiology in Biotechnology and Industry

• Biotechnology is a broad field that uses living organisms/systems to produce products.
• Developments in molecular biology have expanded the scope of biotechnology.
• Industrial use of microbes in biotechnology produces many compounds including insulin and antibiotics.

Biotechnology: Industrial chemicals

• Microbes, like Aspergillus niger, can produce industrial chemicals such as citric acid.
• Proteases from Bacillus licheniformis are used in laundry detergents.

Biotechnology: Natural medicinal products

• Natural products of microbial origin have wide use in therapeutics, including antimicrobials, cholesterol lowering agents, and neurotoxins (e.g. botulinum toxin).

Biotechnology: Recombinant medical products

• Bacteria can be genetically modified to produce therapeutic proteins.
• Recombinant human insulin (Humulin) is an example.
• Recombinant vaccines (e.g., Gardasil) can target human papillomavirus (HPV).

Microbial Spoilage

• Microbes often spoil products by utilizing nutrients, leading to deterioration of the product.
• This can affect pharmaceutical products, targeting raw materials or finished products, causing costs/risks.

Practical microbiology: Growing microbes

• Sterile or liquid media used to grow microbes in the laboratory.

Practical microbiology: Looking at microbes

• Different methods exist for visualizing microorganisms, including the naked eye, and microscopic approaches like light microscopy and electron microscopy.

Practical microbiology: Molecular microbiology

• Extract genetic components (DNA, RNA) for whole genome sequencing.
• Analyze cell components (proteins) for immunological and structural studies.

Classification of Biological entities

• Classification systems categorize organisms based on shared characteristics.
• Organisms are classified into cellular and acellular categories (e.g. Eukarya, Archaea, Bacteria; Viruses, Viroids, Virusoids, Prions).

Taxonomy ranks: Species

• Species are groups of organisms with stable, shared properties, distinct from other groups.
• Strains are subtypes of a species that differ slightly in characteristics.

Phenotype classification in microbiology

• Morphology (shape, cell structure)
• Biochemistry (enzyme production, transport proteins)
• Life cycle (vegetative or spore forming)

Serotype classification in microbiology

• Serotype refers to distinct variations in cell surface antigens within a species. This is often characterized using different identifying antigens (e.g. Kauffman-White classification).

Genotype classification in microbiology

• Genotype refers to a cell's genetic makeup, determining characteristics.
• Genomics (DNA sequencing) can be used to determine this.
• Bacterial species definition uses genomic sequencing with at least 95% identical genomic sequences to determine species. This method is affected by horizontal gene transfer.

Whole genome sequencing

• Determining the complete DNA sequence of an organism at a single time.
• Information such as presence/absence of genes, gene mutations or insertions/deletions can then be used to characterize and assess organisms. (e.g. SNP, RNA) phylogenetic analysis, etc.

Visualizing Genotypes: Phylogenetics

• Phylogenetics studies evolutionary relationships using DNA or protein similarities.
• MSA generates clusters of related organisms and phylogenetic trees from this data to show the relationships between species.

How to work with dangerous bugs and not catch something

• Microbiology practice necessitates strict adherence to Biosafety Levels (BSLs) to avoid contamination.
• Understanding ACDP categories and Biosafety levels is essential for safe handling of microbiological specimens.

Microbial growth and evolution

• How microbes are cultured.
• Different stages of bacterial and viral growth (lag, log, stationary, and death phases).
• Introduction of bacterial evolution and its relevance.

Sources of carbon, energy and electrons

• Microbes require carbon and energy sources for growth and metabolism. Examples of these could include CO2 (used by autotrophs); light (used by phototrophs), compounds, reduced inorganic compounds (used by lithotrophs), organic molecules (used by organotrophs) etc.

In-vitro microorganism culture

• Culturing microbes in a controlled environment outside of their natural habitat (e.g., liquid or solid media)
• The type of media used can determine which microbes grow.

Atmospheric requirements

• Microbes require specific atmospheric environments for growth.
• Examples include obligate aerobes (require oxygen), obligate anaerobes (require absence of oxygen), facultative aerobes (can adapt without oxygen), microaerophiles (need lower oxygen levels) and aerotolerant anaerobes (tolerate oxygen but use fermentation for growth)

Bacterial cell division and growth

• Bacteria can reproduce independently via binary fission or budding.
• Growth proceeds through phases like lag, log, stationary and death. Doubling time differs widely amongst species.

Microbial metabolism

• Primary metabolism involved in central processes such as synthesis of cellular components and energy production
• Secondary metabolism involved in production of non-essential (but beneficial) byproducts such as antibiotics

Laboratory scale culture

• Different culture methods are used dependent on the requirements of the product/requirements to conduct the tests (e.g. batch culture, continuous culture).

Viral replication

• Viral replication relies on the subversion of host replication machinery
• Lytic vs lysogenic replication mechanisms.

Viral replication - types

• Viral replication can be in two ways, Lytic and Lysogenic.

Bacterial evolution: Mutation

• Mutations are permanent changes in a cell's genetic material.
• Mutations can be harmful, beneficial or neutral to the cell.

Bacterial evolution: DNA acquisition

• Bacteria can acquire new genetic material through horizontal gene transfer via several mechanisms (transformation, transduction and conjugation).

Bacterial evolution: Antimicrobial resistance

• Antibiotic usage can lead to selective pressure on bacteria, potentially accelerating the evolution of resistant strains.

Why should I care?: Antimicrobial resistance

• Antibiotic resistance is a serious issue requiring concern due to its potential health risks and implications for healthcare systems. The emergence of drug resistance is a serious concern around the world.

Strain improvement

• Improving bacterial strains to increase production yields/efficiency (e.g. Penicillium chrysogenum) is done in many ways including genetic manipulation, exposing to stressors etc.

Heterologous Gene Expression

• Using organisms (e.g., bacteria) to produce a product that is not naturally produced

Sources of Contamination and Sampling

• Sources of microbial contamination can include environmental sources and personnel.

Controlling Microbial Contamination

• Environmental/Personnel controls reducing the risk of contamination by using methods such as clean rooms, laminar flow cabinets, isolators and PPE, hand washing/disinfection, to avoid contamination.

Aseptic Technique

• Aseptic techniques are used in sterile medicinal products
• Aseptic techniques are extremely critical to minimize contamination

Microbial sampling

• Filtration and direct inoculation for isolating samples. Environmental sampling (surface, contact, air)

Microbiological calculations: Total viable count

• Use haemocytometer or other methods for counting microbes
• Useful for determining numbers of microbes or CFUs in a known area

Regulating Contamination

• Regulatory agencies ensure safety & quality standards in the manufacturing through testing/regulations of products to minimize/detect contamination.

What happens when it all goes wrong?

• Microbial contamination of products can result in product recalls and litigation.

MPharm Programme

• Purification section: focus on different purification method(s), downstream procedures, sterilisation and sterility checking of products/procedures.

Microbial Identification

• Techniques (culture-based and molecular) for identifying microbial contaminants, limitations & advantages.

What is Diagnostic Microbiology?

• Diagnostic microbiology emphasizes identifying the source/cause of infection. This can involve a range of tests and techniques from typing, testing antimicrobials to examining the cells/genotype etc.

Microscopy: Light and Electron Microscopy

• Methods for visualizing microorganisms, using light microscopy (standard staining procedures e.g Gram stains) or electron microscopy.

Molecular Identification: PCR, ELISA, MALDI TOF

• Identification of microbes using various molecular techniques (e.g., PCR, ELISA), MALDI-TOF mass spectrometry.

Disease and Pathogenesis

• Infectious diseases still represent a significant public health problem.
• Factors for risk of developing infectious disease include exposure, age, genetics, etc.

Scale of disease

• Endemic, epidemic and pandemic infectious disease outbreak types exist with varied levels of associated risk

Sources of Disease

• Sources of infectious diseases can include environmental contaminants (water, aerosolized pathogens, soil), animal sources, or other personnel.

Terminology

• Definitions of key terms in infectious diseases including pathogenicity, virulence, and virulence factors, also related concepts relating to microbial infections (e.g. colonization, transmission, immuno-evasion), and others.

Transmission and exposure

• Methods of microbial transmission, including vertical (mother to child), horizontal (person to person), and vector (through other organisms).
• Aspects of exposure including the role of microbes and factors that effect their persistence (e.g. host, environmental, etc..)

Biofilms

• Biofilms are complex communities of microbes which adhere to a surface, leading to increased resistance to treatment and other problems
• Biofilm forming organisms are prevalent, and problematic

Microbial toxins

• Classification of microbial toxins, including exotoxins and endotoxins (e.g. botulinum toxin), the different effects of toxins (e.g. cell death), and how they may affect the host response (e.g. septic shock).
• Different types of microbial exotoxins are mentioned (e.g. cytotoxins, neurotoxins & enterotoxins), their mode of action & effects on the host.
• Endotoxins (e.g. LPS) are also mentioned, their properties, host response, and issues around their removal/detection.

Non-bacterial disease

• Diseases caused by fungi (e.g. athletes foot, thrush, aspergillosis) and viruses discussed.