Horizon Scanning in Microbiology Diagnostics

1. Horizon Scanning in Microbiology Diagnostics Dr Jaisi Sinha Consultant Microbiologist and Virologist NPHS Microbiology, Cardiff

2. Outline of this Presentation • What are the traditional and newer diagnostic methods in microbiology? • What is the role of molecular testing in microbiology? • How do we apply these technologies to impact on patient management?

3. A Microbiologist’s View Clinical Support and Advice Laboratory Diagnosis of infection Patient Management New or resistant infections Antimicrobial agents Outbreak management

4. Laboratory Diagnosis of Infection – Test selection • Selection of a diagnostic test • Specimen, isolate • Speed, specificity • sensitivity • Application, relevance • Is new genuinely better?

5. What are the traditional and newer diagnostic methods in microbiology? • What is the Role of Molecular testing in Microbiology? • How do we apply these technologies to impact on patient management?

6. Traditional and newer methods of diagnosis in microbiology • Microscopy and culture • Identification – phenotypic • Antimicrobial susceptibility – phenotypic • Newer phenotypic based tests • Since HIV- expansion in new molecular testing in virological diagnostics

7. Advantages of traditional methods • Can be catch-all and diagnose mixed infections • Established sensitivity and methods • Living organisms can be recovered

8. Disadvantages of traditional methods • Labour-intensive • Therefore also perceived as expensive and slow • A ‘skilled’ activity – operator dependent • Results may not have a definite identification

9. Molecular diagnostic tests - basic concepts of nucleic acid based tests • The main purpose of amplification (e.g. PCR) is to make a huge number of copies of a gene. • Does not require viable organisms • Can be very sensitive – but contamination issues • For rapidity requires a known target gene sequence • Therefore can miss unknowns • Molecular testing in diagnostic microbiology is usually restricted to detection (qualitative), quantification (viral load), and genotyping. Not usually sequencing • Ability to detect unknown or multiple organisms slower - may take days or weeks and require reference/research laboratory facilities

10. What are the traditional and newer diagnostic methods in microbiology? • What is the role of molecular testing in microbiology • How do we apply these technologies to impact on patient management?

11. What is the Role of Molecular testing in Microbiology • Discovery of new infections at a reference laboratory level • Established clinical application for management of certain virology infections • Its role elsewhere in microbiology?

12. What is the Role of Molecular testing in Microbiology • Discovery of new infections at a reference laboratory level

13. Diagnosis of New and Emerging infections- How is it done in a specialist reference laboratory? • Electron microscopy/immunofluorescence/culture • Obtain a ‘culprit’ organism, visualisation • Extraction, amplification and detection of DNA/RNA sequence – requires broad- range PCR as specific target sequence unknown • Cloning of sequence – purification of PCR product • Sequencing – establish likely unknown target sequence, design PCR assay, phylogenetics • Proteomics – identify virulence factors, phylogenetics, antibody design • ELISA design – serological assays

14. What is the Role of Molecular testing in Microbiology • Established clinical application for management of certain virology infections

15. Molecular Diagnostic Testing-Current Uses in Virology • Routine viral detection • Replacing cell culture – sensitive, quick • BBVs, Intrauterine infections, respiratory viruses, norovirus • Viral Load Monitoring (treatment monitoring) – HIV, HCV, CMV (pre-emptive monitoring) • Genotyping/resistance testing – HIV, HBV, HCV

16. What is the Role of Molecular testing in Microbiology • Its role elsewhere in microbiology?

17. Other currently available diagnostic molecular tests • Fastidious bacteria – C. trachomatis, GC, pertussis, TB, M. genitalium, T. whipplei, C. burnetti, B. henselae • Rapid Bacterial diagnosis – N. meningitidis, S. pneumoniae, H. influenzae • Antibiotic resistance – MRSA, VRE, ESBL, multi-drug resistant TB • Parasites/Fungi – T. gondii, Malaria, P. carinii, Aspergillus

18. Current diagnostic molecular tests- advantages • Rapid diagnosis • Non-culturable, or slow- growing, fastidious organisms • Antibiotic susceptibility • Culture- negative samples • Bacterial typing

19. Current Molecular Diagnostic Tests - Disadvantages • Rapid tests can detect specific organisms only • Do not provide a catch- all in a realistic timeframe • Can be very expensive • Significance of results or test applications not well-established

20. What are the traditional and newer diagnostic methods in microbiology? • What is the Role of Molecular testing in Microbiology • How do we apply these technologies to impact on patient management?

21. Diagnosis of Infection- a few hurdles in the ‘New’ NHS • Immunocompromised patients • ‘New’ or resistant infections • Pathology modernisation, clinical changes and Trust restructuring • Application of traditional, current and new diagnostic tests

22. Meningococcal PCR • Well established test • Management of meningococcal meningitis - clinical diagnosis • Patient care – early (GP) treatment • Public health – early prophylaxis • Results of PCR test Negative – not v.sensitive: continue early abx, prophylaxis Positive – confirms culture negative; serotyping and wider prophylaxis • Application not based on rapidity of test

23. MRSA PCR • Suggested as potential screening tool • 4hr test; batch testing • Sensitivity • Cost • Application of results • Patient cohorting/isolation

24. Hain Strip for Blood cultures • New technology • Identification of specific bacteria • Specific antibiotic sensitivity results • Within 4 hours of a positive blood culture (12-48 hours) • Rapid compared to traditional methods • BUT future impact on patients?

25. Impact on patient care? • Surviving sepsis campaign: effective antibiotic treatment benefit < 1 hours • Less serious infections: effective antibiotics at 24 hours • Where will Hain strip improve on traditional methods for patient outcome? • How can we best apply our resources on improving patient outcomes in the NHS

26. Microarrays in Blood Cultures • The future? • Microchips with newer nucleic acid amplification and detection systems • Enormous potential for catch-all • Rapid identification, antibiotic susceptibility, virulence factors • Self-contained instruments for near-patient diagnosis?

27. Summary • Currently culture methods are still very effective particularly in non-viral diagnostics • Molecular methods can be rapid for specific infections • Currently for mixed infections or unknown infections, pure molecular methods not always superior in a diagnostic laboratory • What if we lose traditional methods in the process? • What impact does the new method have on patient management?

28. ‘Why does this magnificent applied science which saves work and makes life easier bring us so little happiness? The simple answer runs: Because we have not yet learned to make sensible use of it.’ Address, California Institute of Technology (1931)