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.