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

• WHO Quality Laboratory Manual 2011
• Quality management (IDMIC links)
• ISBAR and clinical liaison process

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 Staph. aureus– 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