MICR5829 L15: Commensal Flora 5/12/25

What is this?

-Population of microorganisms that inhabit the skin/mucous membranes of healthy individuals

Commensal flora

What are some microorganisms that might be found in commensal flora?

Bacteria, archaea, fungi, viruses, mites

What are some other words for the commensal flora?

-Symbionts

-Microbiome

When is the commensal flora acquired?

Rapidly after birth

True or False: Commensal flora composition shifts over lifetime

True

True or False: Commensal flora does not cause disease in healthy people most of the time

True

How long do transient flora last?

Hours to weeks

What type of commensal bacteria would you expect to find in the oral cavity?

Anaerobic

What type of commensal bacteria would you expect to find in the Skin flora?

Gram Positive

Name an example of a commensal bacteria type you would most likely find in the Skin flora

Coagulase-negative staphylococci

Name a species of commensal bacteria found in the Small Intestine (upper bowel)

Enterbacteriaeceae

What commensal bacteria would you find in the Large Intestine (colon, lower bowel)?

-Anaerobic

-Both Gram Positive and Negative

What commensal bacteria would you find in the vagina?

-Lactobacilli

-Anaerobic

-Candida (low)

How are commensal flora beneficial?

-Compete for space and nutrients

-Form a colonization barrier

-May produce bacteriocins which inhibit other organisms

-Alter environment to make it unfavorable (e.g. pH)

What is this?

-Colonization resistance

Commensal flora form a colonization barrier

What do commensal flora produce?

Vitamins K, B12

What commensal flora produces Vitamins K and B12 in humans?

Intestinal flora

How do Vitamins K and B12 help?

-Breaks down large molecules

-Helps w/ food absorption

What are some harmful compounds that commensal flora help to degrade?

-Cholesterol

-Toxins

-Drugs

When should you minimize the impact of commensal flora to reduce clinical species contamination?

1) Collection

2) Transport/storage

3) Processing

True or False: Sputum and fecal samples contain both commensal flora and pathogens

True

What skin antiseptic products can minimize specimen contamination during blood collection?

-70% alcohol

-Povidone iodine

How can you distinguish between pathogenic/non-pathogenic during specimen processing?

-Use selective media

-Inhibit commensals, encourage pathogen

What are some body sites that you would expect to have commensal organisms?

-Mouth

-Nose

-Upper RT

-Skin

-GI tract

-Female genital tract

-Urethra

What are some body sites that you would expect to be sterile?

-Blood and bone marrow

-CSF fluid

-Serous fluids

-Tissues

What are some body sites that are not completely sterile, but typically pathogen-free?

-Lower RT

-Bladder

Name some examples of antibiotic resistant organisms

-MRSA (Methicillin)

-VRE (Vancomycin)

-ESBL (Beta Lactams)

When would you order specimens?

-Antibiotic resistant organisms

-Specific pathogens/notifiable diseases suspected

-Chronic/unresolving

When would specimens not be ordered?

-Diagnosis has already been made

-Empirical therapy has started/is working

-Results are unlikely to be meaningful

What is a situation where specimen collection is not necessary because the results are unlikely to be meaningful?

-Too much commensal flora

-Will not contribute to patient care

What ideal specimen characteristic for detecting pathogens is this?

-CSF used for detecting meningitis

-Many guidelines for which specimens to collect for disease/pathogen

1) Appropriate for the disease process

What ideal specimen characteristic for detecting pathogens is this?

-May be obtained after an antibiotic-free period

2) Obtained before antimicrobial agents have been administered

What ideal specimen characteristic for detecting pathogens is this?

-Only pathogen is present

3) Free from contamination with normal flora

What ideal specimen characteristic for detecting pathogens is this?

-Leak proof containers

-Sealable bag, separate paper work section

4) Collected in an appropriate container or transport media

What ideal specimen characteristic for detecting pathogens is this?

-Can tell species name

5) Properly label

What ideal specimen characteristic for detecting pathogens is this?

-If too little, not good

6) Large enough to process correctly

What specimen rejection issue is this?

-Specimen is not labeled

-Too little information

-Information on label does not match the requisition form

1) Labelling issues

What specimen rejection issue is this?

-Improper temperature

-Incorrect medium

-Delays > 2 hours post collection

2) Transport issues

What specimen rejection issue is this?

-Quantity is insufficient

-Leaking or dried up

-Received in a fixative

-Unlikely to yield meaningful results

3) Specimen issues

Why would a specimen being in a fixative be unusable?

No viable organisms present

What is an example of a specimen being unlikely to yield meaningful results?

-Specimen for anaerobic culture from a site with anaerobes as part of the normal microbiota

-Processing specimen would produce information of questionable medical value

What are some bad outcomes caused by poor specimen quality/rejection?

-Delayed diagnosis or misdiagnosis

-Inappropriate antimicrobial therapy

-Increased patient length of stay and hospital cost

What are 3 critical elements for specimen transport?

-Time

-Temperature

-Medium

How soon should a specimen be delivered to lab?

-Within 2 hours

-Must be processed immediately or stored for 24h

What specimens must be processed immediately?

-Shigella (pH)

-H. influenzae, N. gonorrhea, N. meningitidis (temp)

-S. pneumoniae, anaerobes (oxygen)

What specimens are sensitive to pH?

Shigella

What specimens are sensitive to temperature changes?

-N. gonorrhea

-N. meningitidis

-H. influenzae

What specimens are sensitive to oxygen?

-S. pneumoniae

-Anaerobes

How long can a specimen be stored and still used?

24h

What temperature do specimens need to be stored at to prevent microbial growth?

4C

What is a specimen that should not be refrigerated?

-CSF

-Fastidious organisms

What specimen is this?

-Kept at 4°C for no longer than 3 days

-Can alternatively be frozen at ≤-70°C

-Avoid freezing and thawing if possible

Influenza A

What specimen is this?

-Transport to laboratory ASAP

-Should not be refrigerated or exposed to extreme cold, excessive heat, or sunlight

-Transport between 20-35°C • for proper culture results, CSF specimens must be plated within 1 hour

Meningitidis

What do transporting media do?

-Prevent specimen from drying out

-Non-nutritive, stops multiplying

-Buffers stop pH change

How is a semi-liquid consistency achieved?

Adding agar

What transport media is this?

-Semi-solid, good for enteric bacteria

-Lacks any fermentable carbohydrates to reduce risk of pH change

1) Cary Blair medium

What transport media is this?

-Semi-solid, good for fastidious organisms

-Gonococci, streptococci

2) Stuart transport medium

What transport media is this?

-Charcoal absorbs fatty acids that are toxic to N. gonorrhoea

3) Amies charcoal medium

What transport media is this?

-Contains antibiotics and antifungals

-Prevents bacteria and fungi growing

4) Viral transport medium

What transport media is this?

-Anaerobe transport medium, similar to thioglycolate

5) Anaerobe pouch or GasPak

What are some factors that affect swab pathogen viability?

1) Tip (haha)

2) Shaft type

3) Transport medium

True or False: Most swabs are dry and do not require transport medium

False

What type of swab is this?

-Contains fatty acids that can inhibit bacterial growth

-Suitable for non-fastidious bacteria

Cotton-tipped swabs

What are cotton tipped swabs not recommended for?

-Chlamydia, Neisseria gonorrhoea, Bordetella

-Viruses

What type of swab is this?

-Extracted from seaweed

-No fatty acids, may inhibit PCR

-Fine for culture-based detection

Calcium alginate-tipped swabs

What is calcium alginate tipped swabs possibly toxic for?

Lipid-enveloped viruses eg. HSV

What are calcium alginate tipped swabs not recommended for?

-PCR-based detection of B. pertussis

-Covid 19 specimens

What type of swab is this?

-Both are synthetic fibres

-Wide range of uses

-Least toxic swab

-Suitable for both PCR and culture-based detection

Dacron and rayon-tipped cotton swabs

What are some viruses that Dacron and rayon-tipped swabs are recommended for?

Bordetella, N. gonorrhoea, Mycoplasma

What type of swab shaft is this?

-Not recommended for viruses

-Toxic to Ureaplasma, Neisseria spp.

-Can introduce dust/debris

Wooden shafts

What type of swab shaft is this?

-Aluminum or stainless steel

-Used mostly for nasopharyngeal specimens (Bordetella pertussis)

-Aluminum shafts shown to inhibit PCR for B. pertussis

Flexible wire shafts and small tips

What are flexible wire shaft swabs used for?

Male urethral specimens for diagnosis of gonorrhoea

What type of swab shaft is this?

-Inert, no dust

Plastic

What swab shafts are recommended for Covid-19?

-Nylon, Dacron, aluminum or plastic

-Synthetic tipped swabs only

What swab shafts are not usable for Covid-19?

-Calcium alginate

-Wooden

-Cotton

What is the most sensitive method available for detecting organisms in blood?

Culture

How is a blood sample obtained for culture?

-Venipuncture

-Intravascular catheter

Why are multiple blood cultures required to detect bacteremia?

-At least two separate specimens

-Reduce possibility of detecting specimen contaminant

What would a blood culture bottle contain?

-Anticoagulant SPS

-Growth medium

-Compounds for neutralizing antibiotics

What is this?

-Septi-Chek, Isolator, Signal

Manual systems used for incubating blood culture bottles

How do you detect bacteria growth using these systems?

-Septi-Chek, Isolator, Signal

Direct observation

What are these?

-BacT/Alert/BACTEC

Instrumental/automatic systems for incubating blood culture bottles

How do you detect bacteria growth using these systems?

-BacT/Alert/BACTEC

CO2 sensors attached to individual bottles

What is this?

-Required to diagnose meningitis

-Lumbar spinal puncture collection

-Transport immediately at room temp

Cerebral Spinal Fluid (CSF)

True or False: Smaller volumes of CSF are preferred for diagnosis of meningitis

False

What are some other body fluids used for diagnosis?

-Pericardial, pleural, peritoneal, peritoneal dialysis, synovial fluids, serous fluids

-1 to 5 mL

What is this?

-Diagnose infectious diarrhea, food poisoning

-Clean container, tight lid

-5 mL volume minimum

Fecal/rectal swab

True or False: Normal gut flora can acidify GI tract specimens because of carbohydrate fermentation

True

What should you do if a GI tract specimen cannot be processed within 2h?

-Cary Blair transport medium

-Same w/ rectal swabs

What is this?

-Very common specimen

-Used for UTI, cystitis, bladder infection, pyelonephritis (renal parenchyma)

Urine

How is urine specimen obtained?

-MSU (midstream)

-CSU (catheter)

-Cytoscopy collection, suprapubic aspiration

What is this?

-Optimal urine specimen

First-voided morning urine (midstream)

Why is First-voided morning urine optimal?

-Concentrated pathogen

-Midstream, prevents urethral colonizer contamination

How soon should urine specimen be used/how long can it be stored?

-Process within 2 hours

-Store at 4C for 24h

How would you preserve urine specimens if they cannot be processed within 2h?

-Transport tubes

-Buffered boric acid, glycerol, formate, Na

How would you preserve urine specimen bacteria without refrigeration?

-Up to 48h

-Ambient temperature

What is this?

-Used to diagnose range of syndromes

-Many are contaminated with normal skin/UGT flora

Vaginal/urethral swabs

What would you use a high vaginal swab to detect?

-Yeast spp.

-Group B streptococci (pregnancy)

-Trichomonas vaginalis (wet prep)

What would you use a cervical/urethral swab to detect?

-N. gonorrhoeae

-Chlamydia

What would you use a Gram-stained smear to detect?

-Bacterial vaginosis

-Clue cells