Bacteriology 101

Pre-analytical issues

  • Correct indication for testing – concept of ‘diagnostic stewardship’
  • Patient identification and sample labelling
  • Correct specimen collection- avoid contamination- esp. blood culture
  • Correct transport and storage
  • Reject poor samples – sputum with no PMNs squames++, urinary catheters, wound drains, other


  • Media and reagent Quality Control (QC)
  • Antimicrobial Susceptibility Testing QC
  • External Quality Assurance (EQA)
  • Standard Operating Procedures, staff training and competency assessment


  • Timely reporting with efficient communication and storage of results
  • Direct clinical liaison for critical results- positive blood cultures, CSF etc
  • Comments to help interpret results – colonisation/contamination vs significant isolates, AST results – extrapolations , cascade reporting, therapeutic advice derived from standard treatment guidelines


Identification process

  • Presumptive ID characters – Gram stain appearance, culture growth characteristics and colony appearance etc
  • Confirmatory ID  – biochemical, AST, serological or molecular methods usually; often cannot rely on a single biochemical parameter – e.g. optochin susceptibility for pneumococcus or mannitol fermentation for Staphaureus– approx. 5% of strains will be atypical and not show the expected result!

Phenotypic methods

  1. Point of Care (POC) methods – ICTs etc, microscopy is also a potential POC (rapid) test – e.g. gonococcus smear in STD clinic or a pus smear from an abscess
  2. Microscopy
  3. Culture
  4. Rapid tests – indole, catalase, oxidase etc
  5. Biochemistry kits- API, VITEK
  6. Antimicrobial susceptibility- some intrinsic resistance characters help to identify bacteria- e.g. all Gram negatives are vancomycin resistant
  7. Latex Particle Agglutination – e.g. Lancefield grouping for betahaemolytic streptococci
  8. MALDI-TOF (mass spectrophotometry)

Genotypic methods

  1. POC methods – PCR based- different formats – LAMP, GenXpert etc
  2. Conventional PCR – e.g. presence of nuc gene in species indicates it is Staph. aureus
  3. Sequencing – ribosomal 16S variable regions sequenced to locate signature sequences associated with specific bacterial species (18S sequencing for fungi)
  4. MLST typing– global and local epidemiology – eg. ESBL ST131 coli , KPC carbapenemase-containing ST258 Klebsiella pneumoniae
  5. Whole genome sequencing of isolate(s)– can be used to provide an in silico MLST or survey of resistance genes


About mdjkf

Microbiologist and Infectious Diseases Physician
This entry was posted in Module-basic microbiology and AMR and tagged . Bookmark the permalink.

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