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

Analytical

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

Post-analytical

  • 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

References

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

strep-a

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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