Microbiology Lectorial Notes

Lectorial Introduction

  • The term 'lectorial' reinforces theory for better understanding.
  • Questions can be typed in the chat for monitoring during pauses.

Textbook and Case Studies

  • Access the textbook electronically in the library.
  • Case studies are available for following along, even without prior reading.

Urine Collection and Flora

  • Urine passes through the urethra, which contains skin flora.
  • Skin flora composition varies based on age and antibiotic usage.
  • Gram negatives from the bowel are less common around the urethra due to dryness; however, tight clothing can promote their survival.
  • First part of urine washes away skin organisms, potentially including gram negatives.

Early UTI Studies

  • Less than 1,000 organisms per milliliter (mL) often indicates contamination.
  • Greater than 100,000 organisms per mL is highly predictive of a UTI.

Semi-Quantitative Culture in the Lab

  • A loop is used for semi-quantitative culture, dispensing approximately one microliter (\muL).
  • 1 \mu L requires a multiplication by 1,000 to equal 1 mL.
  • Micro signifies a factor of 1,000 (think of microscope magnification).

Applying Colony Counts

  • Contamination Threshold: 1,000 organisms/mL or less.
    • One organism on the plate (using a 1 \mu L loop) equates to 1,000 organisms/mL.
  • UTI Probability: Greater than 100,000 organisms/mL
    • Greater than 100 colonies on the plate indicate a higher likelihood of UTI (100 x 1,000 = 100,000).

Calculation Examples

  • 10 colonies on the plate = 10 \times 1,000 = 10,000 organisms/mL (10^4).
  • Greater than 100 colonies = Greater than 100 \times 1,000 = 100,000 organisms/mL (Greater than 10^5).
  • Practice converting colony counts to organisms per mL to prepare for practical questions.

Self-Check Applications

  • If colony count is greater than 10^4 per mL, there are generally more than 10 colonies on the agar.
  • Greater than 100 colonies suggest a probable UTI, while greater than 10 suggests a possible UTI.
  • The presence of only one type of organism increases the likelihood of a probable UTI.

Microscopy Considerations

  • The absence of white blood cells should be considered and commented on.
  • Laboratories have standard operating protocols for reporting results.
  • Susceptibility is favored over sensitivity due to legal implications.

Mixed Organisms

  • Two organisms present with one predominant (greater than 100 colonies) and white blood cells suggest a possible UTI.
  • Skin organisms may be difficult to detect on agar, potentially affecting diagnosis.
  • Test questions will accept either probable or possible UTI in such ambiguous cases.

Staphylococcus Saprophyticus

  • Staph. saprophyticus is the second most common cause of UTI in young women.
  • It can split urea, making it well adapted to the urinary environment.

Multiple Organisms

  • With more than two organisms, follow-up is recommended only for suprapubic aspirates.

Suprapubic Aspirate

  • Suprapubic aspirates are pertinent for irritable, febrile babies when pediatric bag urine samples show multiple organisms and white blood cells.
  • Important to rule out UTI to prevent kidney complications.
  • Suprapubic aspirate questions won't feature in assessment, but knowledge of what they are and paediatric bags are expected.

Agar Plate Practice

  • Identify beta-hemolytic and lactose-fermenting organisms.
  • Estimate colony counts (e.g., 20 lactose fermenters or E. coli).
  • Group B or D streptococci are common UTI causes.

Colony Counting

  • For example: 10, 20, 30…80, and probably greater than 100 colonies.
  • May classify as more than 100 \times 10^3 organisms/mL or greater than 10^5 \times 10^3 per liter.

Additional Evidence

  • Squamous epithelial cells (SEC) indicate a potential contamination.
  • High SEC count with Group B Strep suggests probable contamination.
  • Report findings, including organism counts and SEC presence, with a comment suggesting sample recollection if necessary.

Contamination in Suprapubic Aspirates

  • Suprapubic aspirate contamination is rare, but always consider it.
  • Transport conditions affect sample integrity (e.g., delays at nursing homes).

Determining Contamination

  • Number of organisms present.
  • Potential delays in transport.

Case Study: Six-Month-Old with Fever

  • Fever in a six-month-old suggests risk of kidney infection.
  • Dipstick: Leukocytes positive, nitrates negative (bacteria may not produce nitrates).
  • Positive leukocytes mean sample should be sent to the laboratory.
  • Take pediatric bag urine sample first, instead of an immediate suprapubic sample.

Expected Microscopy Outcomes

  • White blood cells.
  • Possible red blood cells (if there is inflammation).
  • Potential presence of fecal matter.

Culture Outcomes

  • E. coli is the most common cause of infection.

Direct Susceptibility Tests

  • Direct susceptibility: Inoculate plate directly with urine sample using a Lawn Inoculum and using Antibiotic Discs, without waiting for the organism to grow.
  • Standard Susceptibility Testing: Organism is grown on a plate; a defined inoculum is selected; a suspension is created, and plates are inoculated in a standard fashion.
  • If there is a big mixture do not report direct sensitivities.
  • Useful for urgent cases (e.g., fever in a young child) but requires careful interpretation (discuss with demonstrator).

Identifying Infecting Organism

  • Chrome agar aids identification by color.
  • Standard operating protocol dictates confirmation tests (e.g., MALDI-TOF for resistant organisms).

Long-Term Implications

  • Kidney infection is a critical concern.

Antimicrobial Prescribing Policy

  • Policies control antibiotic usage to prevent resistance.

Antibiotic Stewardship

  • Laboratories adhere to antimicrobial stewardship to guide antibiotic use.

Antibiotic Choices (Kefuroxime)

  • Kefuroxime is a broad-spectrum cephalosporin.
  • Clinician used a high tier antibiotic early, which is non-ideal antibiotic stewardship.
  • Kefuroxime can disrupt gut flora, leading to Clostridioides difficile (C. diff) infection.
  • Narrow spectrum antibiotics such as Trimethoprim are ideal because your immune system uses the drug's effects of slowing down bacteria from reproduction, to clear the microoganisms.

Intravenous Antibiotics

  • Require hospitalization and increase risk of C. difficile infection.

Suitable Antibiotics for E. Coli UTI

  • Assess patient sickness.
  • Urinary antiseptics (e.g., nitrofurantoin) can be effective for mild cases.
  • * Nitrofurantoin is a urinary antiseptic, and not for kidney infections or sepsis.
  • Trimethoprim slows down bacteria, allowing the immune system to clear the infection; is a very good choice.

Reporting Antibiotic Lists

  • Avoid excessively short or long lists to balance restriction and effectiveness.
  • Multidrug resistance is a consideration.

Hip Replacement Patient (Mr. Smith)

  • More prone to infection due to catheter use post-surgery.
  • High white cell count, resistant E. coli (sensitive to nitrofurantoin) presents a dilemma.
  • Avoid nitrofurantoin if loin pain indicates kidney involvement.
  • Higher-level cephalosporins and gentamicin may be necessary.
  • Pyrexial = fever

Hospital Readmission

  • Low blood pressure indicates possible sepsis (medical emergency).

Sample Collection

  • Collect blood cultures.

Urgent Reporting

  • Communicate results to the clinician promptly.

Empirical Treatment

  • Start with third-generation cephalosporin; gentamicin as an alternative.

Additional Clinical Investigations

  • Full blood count (hematology).
  • Assess inflammation (CRP).
  • Urea and electrolytes (biochemistry).
  • Consider lactate level test (though not covered in the test).

Foley Catheter

  • Balloon design prevents dislodgement.
  • Collect urine from the tube after clamping to prevent contamination from stagnant urine in the bag (collection via tap for urine samples is not viable).

Agar Plate Analysis

  • If pink colony is indole positive: greater than 10^5 organisms/mL of E. coli.
  • Tiny white colonies: suspected skin flora (approximately 20 by 10^5).
  • Consider white cell count and potential contamination.
  • Select well-separated colonies on the edge for susceptibility testing.