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Horizon Scanning in Microbiology Diagnostics. Dr Jaisi Sinha Consultant Microbiologist and Virologist NPHS Microbiology, Cardiff. Outline of this Presentation. What are the traditional and newer diagnostic methods in microbiology?

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horizon scanning in microbiology diagnostics

Horizon Scanning in Microbiology Diagnostics

Dr Jaisi Sinha

Consultant Microbiologist and Virologist

NPHS Microbiology, Cardiff

outline of this presentation
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?
a microbiologist s view
A Microbiologist’s View

Clinical Support and Advice

Laboratory Diagnosis of infection

Patient Management

New or resistant infections

Antimicrobial agents

Outbreak management

laboratory diagnosis of infection test selection
Laboratory Diagnosis of Infection – Test selection
  • Selection of a diagnostic test
    • Specimen, isolate
    • Speed, specificity
    • sensitivity
  • Application, relevance
  • Is new genuinely better?
slide5
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?
traditional and newer methods of diagnosis in microbiology
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
advantages of traditional methods
Advantages of traditional methods
  • Can be catch-all and diagnose mixed infections
  • Established sensitivity and methods
  • Living organisms can be recovered
disadvantages of traditional methods
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
molecular diagnostic tests basic concepts of nucleic acid based tests
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
slide10
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?
slide11

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?
slide12

What is the Role of Molecular testing in Microbiology

  • Discovery of new infections at a reference laboratory level
slide13

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
slide14

What is the Role of Molecular testing in Microbiology

  • Established clinical application for management of certain virology infections
slide15

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
other currently available diagnostic molecular tests
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
current diagnostic molecular tests advantages
Current diagnostic molecular tests- advantages
  • Rapid diagnosis
  • Non-culturable, or slow- growing, fastidious organisms
  • Antibiotic susceptibility
  • Culture- negative samples
  • Bacterial typing
current molecular diagnostic tests disadvantages
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
slide20
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?
diagnosis of infection a few hurdles in the new nhs
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
meningococcal pcr
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
mrsa pcr
MRSA PCR
  • Suggested as potential screening tool
  • 4hr test; batch testing
  • Sensitivity
  • Cost
  • Application of results
    • Patient cohorting/isolation
hain strip for blood cultures
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?
impact on patient care
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
microarrays in blood cultures
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?
summary
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?
slide28
‘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)