Microbiology Review

Microscopy is to identify the pathogen.

Gram Staining

High sensitivity to determine the presence of gram-positive and gram-negative bacteria by exploiting the different morphology of the cell wall. The thicker peptidoglycan wall of gram-positive bacteria trap crystal violet and can not be washed of with alcohol in contrast to bacteria with a thin peptidoglycan layer in the cell wall. This is the foundation of gram staining.

Interpret results:

containment vs coloniser vs pathogen
cultured bacteria does not = antibiotic required.
Sterile sites (Blood, CSF, Joint fluid) NO bacteria should grow here
Non-Sterile sites (Sputum, skin, faeces)Bacteria is normal

Potential pathogen vs colonising flora

Growth and Physical Characteristics

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Important gram-positive pathogens

Cocci Clusters
-staphylococcus aureus (Skin, soft tissue, abscesses, HAI bacteraemia, sepsis.)
-Coagulase negative staphylococcus (Infection of prosthetic devices inc. lines)
Cocci Chains
-Enterococci (UTI, endocarditis and peritonitis (usually polymicrobial))
-Group A streptococcus S.pyogenes (cellulitis, fascititis, pharyngitis and rheumatic fever.
-Group B streptococcus s.agalactiae (neo-natal Cellulitis, Septic Arthritis)
-Group C & G Streptococcus (Cellulitis, Septic Arthritis)
-Group F Streptococcus (Abscesses in the hepatic, brain and endocarditis)
-Viridian streptococci (Dental, subacute endocarditis)
Diplococci
-Streptococcus pneumoniae (Pneumonia, Meningitis, otitis media)

Important gram negative pathogens

-Escherichia coli (UTI/pyelonephritis, cholangitis, diverticulitis)
-klebsiella pneumoniae (UTI/pyelonephritis, cholangitis, diverticulitis, liver abscess and hospital associated sepsis or infection.
-pseudomonas aeruginosa (hospital associated line sepsis, Catheter associated UTI, ventilation associated)
-Heamophilus spp. (Pneumonia, Meningococcal disease)
-Neisseia meningitids (Meningitis, meningococcal)
-Neisseia gonorrhaeae (urethritis/cervicitis, disseminated disease)
-salmonella spp. Shigella, campylobacter (gastroenteritis, sepsis)
Burkholderia, yersinia, brucella, pasturella

Guiding treatment

Based of normal flora vs abnormal flora

Pathology = Syndrome + predominance + CRP
If Bacteria are in a blood culture this is alway a concern, could also still be contamination. Take two cultures.

AMS role in Micro

Narrowing spectrum of therapy based on susceptibility testing.

Not working up contaminants.
-Enterococcus sp in skin swabs
-candida sp from sputum
-enterobacterales in sputum
-low urine colony counts without pyuria
-coagulase neg staph (staphylococcus epidermidis) in blood cultures

Resources and Readings

Dr David Philip Garner, Microbiology Nuts & Bolts (2013)