Microbiology Lecture Notes: Chapters 1-7

Genus, Species, and Strains

• Organisms are classified by genus and species. Every living organism can be described this way, and bacteria follow the same rule.

• Examples mentioned:

  • Escherichia coli (E. coli)

  • Staphylococcus aureus (S. aureus)

  • Streptococcus species (S. pyogenes is the proper shorthand for Streptococcus pyogenes; the transcript also mentions a mispronounced or mistaken form like "S iogenes" and emphasizes familiarity with correct names).

• Mispronunciations or informal forms can cause confusion (e.g., "oranges" is likely a mis-speech for "organisms"). Recognize the intended organism: genus + species, not just a common name.

• Strains are subtypes within a species. All strains belong to the same genus and species but differ in certain attributes.

• Example strains of E. coli discussed:

  • A typical benign or non-pathogenic strain.

  • E. coli O157:H7 (often referred to as "E. coli O157" in shorthand within the transcript). This strain is pathogenic and can cause severe illness or death in some cases.

• Why strain-level differences matter: strains can differ in traits such as antibiotic resistance, virulence, or toxin production. All are still E. coli, but they are not identical.

• When diagnosing infections, clinicians must consider the specific strain because not all strains respond to the same antibiotics.

• Practical implication: a single species can include multiple strains with markedly different clinical outcomes.

Bacterial Reproduction and Genetic Variation

• Bacteria reproduce asexually via binary fission: a single cell copies its DNA and divides to produce two daughter cells.

• In theory, progeny from binary fission are identical to the parent.

• However, real populations experience genetic variation through:

  • Mutations: random DNA changes during replication.

  • Gene transfer: exchange of genetic material between bacteria (to be discussed in greater detail later). This contributes to genetic diversity beyond simple mutation.

• Because of mutation and gene transfer, progeny are not perfectly identical to the parent over time, leading to the emergence of new strains.

Strains: Definition and Examples

• Strains are subgroups within a species that have distinct genetic attributes or behaviors.

• They can arise from:

  • Mutation during replication

  • Gene transfer (horizontal gene transfer) — methods include transformation, transduction, and conjugation (details discussed later in the course).

• The transcript provides concrete example:

  • A strain of E. coli may be mild and cause no illness.

  • Another strain, such as E. coli O157, can cause food poisoning and severe illness, potentially fatal in some individuals.

• Not all strains within a species respond to antibiotics in the same way; antibiotic susceptibility can vary by strain.

• Practical takeaway: identifying the exact strain is crucial for selecting effective treatment.

Antibiotic Susceptibility and Clinical Relevance

• When a patient presents with an infection, clinicians must determine which antibiotics will be effective against the specific strain causing the infection.

• Because strains differ in antibiotic resistance profiles, empiric therapy (treatment before exact strain identification) may not always be appropriate; antibiotic choice should consider likely strains and be adjusted once the strain is identified.

• This underscores the importance of:

  • Strain identification in clinical microbiology

  • Antibiotic susceptibility testing for each strain

  • Understanding that resistance can emerge via mutation or gene transfer

Real-World and Hypothetical Scenarios

• Scenario 1: Within E. coli, one strain remains susceptible to a given antibiotic, while another strain has acquired resistance.

  • Possible outcome: treatment success with the antibiotic for the susceptible strain, but failure for the resistant strain.

• Scenario 2: A mutation arises that confers resistance to an antibiotic in a circulating E. coli strain.

  • The resistant strain can spread or persist if not properly controlled, leading to more difficult-to-treat infections.

• Scenario 3 (pathogenic example): E. coli O157 can cause severe foodborne illness, illustrating how a subset of strains within a species can have much higher virulence.

• Mechanisms (to be explored later): mutation and gene transfer are key pathways by which bacteria acquire resistance or new traits.

Lab Schedule and Workflow

• Lab usage and class logistics discussed:

  • Monday labs: typically start around 11:00 but class goes until 12:15; there is another class at 12:30 down the street.

  • To accommodate travel, aim to finish lab a bit before 12:15 on Mondays.

  • Lab work usually begins as soon as everyone has arrived downstairs; the official start time is around 11:00, but the instructor starts earlier when feasible.

  • The length of each lab session varies depending on the activity:

  • Some days you may be able to complete tasks within the hour and a quarter (75 minutes).

  • Other days you may only be able to work for a shorter period (e.g., half an hour).

  • Common activity: streak plates to culture bacteria; other days the results may not be obtained until the next lab session.

• Practical implication: always be prepared for variable lab durations and plan your time accordingly.

• Scheduling note: after class, the group will go downstairs to lab; the usual flow is to begin work promptly, then adapt depending on what can be completed that day.

Key Terms and Concepts

• Genus: a rank in the biological classification that groups closely related species.

• Species: a basic unit of classification; organisms within a species share common traits and can interbreed (in many contexts for bacteria, defined by genetic similarity).

• Strain: a genetic variant or subtype of a microorganism within a species.

• Binary fission: asexual reproduction by division of a single cell into two identical cells.

• Mutation: a heritable change in DNA that can lead to variation among progeny.

• Gene transfer: movement of genetic material between organisms, contributing to genetic diversity and the creation of new strains (to be explored in more detail later).

• Antibiotic resistance: a trait where bacteria are less susceptible or immune to the effect of an antibiotic, often arising through mutation or gene transfer.

• E. coli O157 (O157:H7): a pathogenic strain of E. coli associated with severe illness; serves as a key example of how strains within a species can differ dramatically in virulence.

• Staphylococcus aureus (S. aureus) and Streptococcus pyogenes (S. pyogenes): example genera/species used to illustrate naming conventions and potential confusion with abbreviations.

• Streak plates: a common microbiology technique used to isolate bacterial colonies for study.

Quick Reference: Mathematical Note

• Bacterial population growth over generations can be modeled (in the absence of limitations) by:

• N = N_0 \cdot 2^{g}

  • where:

  • $N$ is the population size after $g$ generations,

  • $N_0$ is the initial population size,

  • $g$ is the number of generations that have occurred.

• This formula illustrates how quickly bacterial populations can expand and why rapid growth and genetic variation (via mutation and gene transfer) can lead to diverse strains within a short time period.