Culture Free Microbiology. Stephen Gillespie Sir James Black Professor of Medicine University of St Andrews

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1 Culture Free Microbiology Stephen Gillespie Sir James Black Professor of Medicine University of St Andrews

2 What does microbiology do? IdenEfy the infeceng organism - Diagnosis SuscepEbility teseng Advise Treatment IdenEfy clustered organisms over- represented in the community- InfecEon Control

3 Why do clinicians not use microbiology results? The speed of progression of infeceon is much faster than the Eme taken to generate results They do not understand the implicaeons of the data 3

4 Culture based diagnosis Slow and likle changed from the Eme of Koch Many organisms do not grow on agar Specimens rendered negaeve by anebioecs Missed diagnosis InfecEon aeeology not understood Missing prognosec informaeon

5 Koch based diagnosis? Presence of a pathogen equals the diagnosis? More than one pathogen responsible for a disease syndrome MulEple pathogens may interact to cause disease OOen likle disenceon between pathogen and commensal New pathogens are emerging and new understanding of pathogens is developing

6 What do we do? Specimen types Urine Wound Swabs Faeces Sterile fluids (including blood culture and pus) Challenges Many paeents could be managed by a clinical algorithm and many specimens e.g., CSU of doubxul value Treatment rarely indicated and usually surgical MulEple pathogens requiring intensive effort and skill Laboratory ideneficaeon ooen occurs aoer the crisis has passed so empiric treatment the norm

7 Respiratory bacteriology Specimen from CAP paeent Final Report Time 0 Time +24 hr Time 36 h Time + 48 hr

8 Co- infeceon 18/80 Virus+ bacteria 15/18

9 Mycoplasma amphoriforme Novel respiratory Mycoplasma sp. Standard methods failed to detect this organism until 1999 Fastidious culture requirements M. amphoriforme Atypical colony appearance M. salivarium

10 LRTI Study Streptococcus pneumoniae 18.8% Haemophilus influenzae 6.3% M. amphoriforme 5.7% Moraxella catarrhalis 1.3% Mycoplasma pneumoniae 1.3% Chlamydia pneumoniae 0% Legionella pneumophila 0%

11 Genera3on 3me of selected mycoplasmas Published data for different experimental se<ngs (in vitro culture media and cell lines) Experimental data for Mycoplasma spp. in vitro growth in Oxoid medium and ME medium M. gallisep6cum 3.50 M. gallisep6cum Mycoplasma species U. urealy6cum M. pneumoniae M. hominis M. genitalium Mycoplasma species M. pneumoniae M. hominis M. genitalium M. amphoriforme * M. amphoriforme Genera3on 3me (h) Genera3on 3me (h)

12 Diagnosis of S. pneumoniae by Optochin suscepebility Diagnosis by bile solubility Bile + lyt+ bacterium = dissolueon of culture But test is difficult to perform and rarely used in clinical pracece 2% S. pneumoniae are optochin resistant S. mi6s can be optochin suscepeble

13 comc primers sequence speciaeon

14 Regulatory region (5 ) relaeve inter- serotype conservaeon High degree of intra- serotype sequence diversity Serotype 6B InserEons/deleEons Difference in degree of sequence variaeon between different serotypes (6B vs. 19F 19A) Serotypes 19F and 19A

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16 Processing pathway for empyema Empyema specimen S. pneumoniae rtpcr S. aureus rtpcr Prevotella spp. rtpcr S. intermedius S. constellatus S.anginosus

17 Maldi a posi3ve step Rapid ideneficaeon of bacteria Does not provide suscepebiliees Delayed by slow growth Of no value if anebioecs render cultures negaeve 17

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19 Molecular suscepebility teseng PCR rpob katg genes from M. tuberculosis HybridisaEon stage against various common mutaeons Rapid and idenefies most MDR strains

20 InfecEon control

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25 Barriers to progress Current microbiology laboratories are orientated towards large volume low cost teseng Few hospitals perform NAT and sequencing Molecular diagnosecs are perceived to be expensive! We have invested in the past!

26 But molecular diagnos3cs is too expensive! Lab automaeon of culture costs more than 1.5m The cost of the wrong treatment is not included The cost of unnecessary tests is not included The cost of addieonal days in hospital is not included The excess of mortality is not included

27 Molecular diagnosis Is cheap WGS price is falling Single cell methodologies are emerging Analysis of mixed samples is emerging WGS provides phenotypic data including toxins and sucepebiliees WGS embeds infeceon control informaeon into the system

28 AlternaEve approach Early interaceon idenefies paeent clinical risk Focus the mind of the non- specialist clinician on infeceon diagnosis Improves the quality of early treatment choices End the fire and forget approach to laboratory invesegaeon

29 Do we always need to culture? 3 typical symptoms of UTI dysuria; urgency; frequency, polyuria; suprapubic tenderness; haematuria AND No vaginal discharge or irritation 90% culture positive Give empirical antibiotic treatment Mild or 2 symptoms of UTI (as above) Obtain urine specimen Examine Urine NOT cloudy 91% negative culture DO NOT TREAT Perform dipstick test with nitrite* positive nitrite +/- leucocyte +/- protein nitrite, leucocytes protein, blood all negative 95% NPV negative nitrite positive leucocyte 14 negative nitrite & leucocyte positive blood or protein Probable UTI UTI very unlikely Probably urethral syndrome Review time of specimen* UTI or urethral syndrome Consider other diagnosis 14 Treat with first line agents on local guidance 5 Reassure and give advice on management symptoms Treat if severe symptoms and send urine for culture

30 Next steps Reduce specimen throughput Review clinical diagnosec pathways to idenefy the clinical gains of rapid diagnosis Set teseng TAT Review and revise the skill mix of laboratories Develop new techniques to fill the diagnosec gaps Reorganise delivery of infeceon diagnosis

31 Molecular diagnosis can not be applied in the same way in all places District general hospitals: high throughput infeceons Regional laboratories: lower throughput and typing NaEonal reference: rare organisms and complex typing methodologies

32 District General Hospitals Real Eme plaxorms Validated tests usually kit based Expert support Referral system to Regional laboratories Tests where a rapid turn around will help e.g., LRTI, viral diseases, MRSA, sterile fluids

33 Regional Laboratories Able to pool populaeon catchment areas for rarer diseases Specialist molecular faciliees and academic backup Suitable for rapid typing e.g., M. tuberculosis or Salmonella. Diagnosis of rarer diseases e.g., meningococcal infeceon, Bordetella pertussis.

34 Conclusions: The challenge of new Genomics revolueon is opening new horizons in diagnosecs There is a significant gap between what is possible today and what is happening This gap is to the disadvantage of our paeents resuleng in unnecessary morbidity and mortality technology

35 Any ques3ons 35