Shift from culture screening to molecular testing

Transcription

1 Shift from culture screening to molecular testing Dr Panagiotis Pantelidis Lead Clinical Scientist / POCT and Clinical Trials Scientific Lead (Immunology / Virology) Pathology - Infection and Immunity Imperial College Healthcare NHS Trust North West London Pathology London

2 Diagnostic Tests Diagnostic testing is an integral part of the healthcare system 75% of clinical decisions are based on a diagnostic test Main drivers of change in a testing strategy are: Demand for quicker, more accurate diagnosis Improvements in efficiency, speed and accuracy of diagnostic tests From the patient point of view - early detection and diagnosis can prevent unnecessary pain and suffering.

3 Obstacles to New Diagnostic Tests Widespread adoption of new diagnostic tests from first evidence typically takes around 10 years Adoption of improvements in technology takes 6 to 12 months. Adoption of new diagnostic tests depends on Clear research evidence to aid decision makers approving new tests. Whether the technological advances match clinicians needs Whether the new test will have a significant impact on current clinical practice. The Royal College of Pathologists has endorsed the Choosing Wisely campaign, to ensure only the most appropriate and effective investigations are used.

4 Genomics The field of genomics has witnessed an explosion of rapid advances over the past 20 years. Generating sequencing data is no longer a limitation. Nucleic Acid Amplification Testing (NAAT) is becoming the cheapest way to produce novel diagnostic tests in infectious diseases Because of scalability - NAAT is the preferred method to deliver large volume national screening programmes

5 Cost is not the limiting factor The cost of molecular diagnostic tests has been driven down by Intense competition between companies Consolidation of patholgy services Expiration of the Roche core PCR patent 28-March-2005 Other companies can use the available bioinformatic algorithms for PCR based NAAT design to deliver robust new tests quickly. Increase in Sequencing data availability in public databases making NAAT design reliable

6 Number of identified microbial species from 1979 to 2012 In 1980, only 1,800 validated bacterial species had been published, whereas more than 500 new species are now described annually PCR amplification and highthroughput sequencing has revealed a much larger microbial world than was believed to exist a few years ago Pierre-Edouard Fournier et.al. Nature Reviews microbiology Vol11; 2013

7 Microbial Causes of Infection Infections may be caused by Viruses (virology) bacteria (inc. mycobacteria, chlamydiae, mycoplasmas, & rickettsiae) (Micro) fungi, (Micro) parasites. (Micro) Some infectious diseases are distinctive enough to be identified clinically Most pathogens can cause a wide spectrum of clinical syndromes in humans. A single clinical syndrome may result from infection with any one of many pathogens. (e.g. Influenza virus infection - respiratory syndromes indistinguishable clinically from streptococci, mycoplasmas, or more than 100 other viruses)

8 From Culture to Molecular Diagnostics Culture has been in the centre of service delivery in both Microbiology and Virology Molecular diagnostics is now an integrated component of virology and microbiology diagnostics The degree integration has not been equal in the two disciplines.

9 Microbiology Anton van Leeuwenhoek described the first bacteria almost 300 years ago (microscopic observation). By the 1890s the culture media used today, Petri dishes, peptones and agar, were developed. Today, Louis Pasteur, (1800s), would feel at home in a diagnostic Micro laboratory

10 Virology Viral isolation was a routine technique for several years in diagnostic virology labs Virus isolation in cell culture dates in the 1900 (Weller and Enders in 1948 and Enders et al. in 1949) Today cell culture/isolation is restricted to reference laboratories

11 Viral Cell cultures Virus Herpes Simplex VZV & Rhinovirus CMV Adenovirus Poliovirus Coxsackie B Echo Influenza A & B Parainfluenza Mumps RSV Measles Rubella Susceptible Cell Lines Vero Hep 2, human diploid (HEK and HEL),human amnion human diploid (HEL, HEK) human diploid fibroblasts Hep2, HEK, MK, BGM, LLC MK2, human diploid, Vero, Hep 2,Rhadomyosarcoma MK, BGM, LLC MK2, vero, hep 2 MK, BGM, LLC MK2, human diploid, Rd MK, LLC MK2, MDCK MK, LLC MK2 MK, LLC MK2, HEK, Vero Hep 2, Vero MK, HEK Vero, RK13 Virus Isolation involves Primary cells -subcultured only once or twice e.g. primary monkey or baboon kidney Semi-continuous diploid cells - can be subcultured 20 to 50 times Continuous cells - derived from tumours of human or animal tissue

12 Viral Cell culture (isolation) No one cell culture can support the growth of all clinically relevant viruses Requires maintenance of several cell types Many clinically important viruses don t grow in cultures suitable for a diagnostic lab Cell cultures are typically viewed microscopically to detect cytopathic effects (CPE ) Examination every 1 2 days -first week post inoculation. CPE detection is highly variable 1 2 days for herpes simplex virus (HSV) to 1 3 weeks for CMV

13 Today We stopped viral cultures in 2011 and our Clinical colleagues have not missed them With today s standards Viral isolation is slow and expensive -result often peripheral to clinical decision-making. NAAT have superior characteristics for routine diagnostic virology Detect, quantify and determine viral mutations directly from primary samplesm with fast TAT, without the need for isolation of the virus in cell culture

14 Not surprising For a new diagnostic technology to become a mainstream diagnostic tool it has to show that it is Faster, Better, Cheaper than existing alternatives Better The iron triangle (Daniel Goldin NASA) Faster Cheaper

15 NAAT tests in Virology Faster - NAAT tests provide a result from primary sample from 20min to 2h Better Greater sensitivity and specificity of NAAT than culture Cheaper Basic HIV-1 viral load Cheaper - you do not need maintain cell culture skills and facilities Cheaper - early result / early intervention / high health economic impact Cheaper Guide targeted therapy to patients who will benefit E.g. Limiting use of Maraviroc to patients with HIV-1 CCR5 tropic viruses and not CXCR4 tropic virus Cheaper - Antiviral resistance can be rapidly identified by NAAT& sequencing and change treatment. HIV-1 antiretroviral mutations

16 Additional advantages NAAT are easily expandable NAAT can be fully automated NAAT can be used to move diagnosis/monitoring to near patient setting and at the point of care NAAT can deliver robust tests for the detection of emerging infections very quickly (Swine Flu, Zika, SARS)

17 NAAT testing Improved Virology services Primary role for diagnostic NAAT is to identify disease and enable management of the patient Qualitative test are used as screening tests Quantification are used to stage disease activity, progression, and monitor efficacy of therapy. Genotyping is used to guide treatment and can have prognostic value. E.g. human papillomavirus (HPV) types 16 and 18 are associated with high-risk progression to neoplasia Resistance mutation testing can change therapeutic intervention Beyond pathogen identification a rapid result can support Infection control / Surveillance /Public Health, delivering an early diagnosis in order to prevent or reduce the spread of hospital acquired infections. E.g. Seasonal respiratory virus viral surveillance to understand circulating viruses.

18 Respiratory Virus Surveillance

19 NAAT technology has evolved Today, the majority of NAAT virology diagnostic tests in the market utilise Polymerase Chain Reaction (PCR) in combination with internal reporter probes (Taqman) referred to as Real-Time PCR. Real-time PCR has proven to be simple, fast, highly sensitive and specific, reproducible, cost-effective, and versatile Other Technologies developed in order to circumvent PCR patent licencing restrictions not widely used commercially: Nucleic acid sequence-based amplification, strand displacement amplification, transcription-mediated amplification, branched DNA amplification, loopmediated amplification, and helicase-dependent amplification

20 NAAT instrumentation has evolved

21 Molecular testing is not all a bed of roses Adopting molecular testing is not without challenges Quantitative molecular assays are still highly variable and require additional standardization and rebasing when changing providers Technically, there are few but valid concerns about False-negative results due to viral genetic diversity Viral load bleeps due to Viral/Pro-viral sampling variations (HIV-1). The clinical significance of viral co-infections and the persistence of viral signals beyond the acute presentation of clinical disease. POC testing brings its own unique challenges

22 Laboratory Microbiology At an elementary level, the clinician needs the answers to 3 very basic questions from the Microbiology laboratory: Is the patient s illness caused by a microbe? If so, what is it? What is the susceptibility profile of the organism so therapy can be targeted? Culture will provide all these answers

23 Virology / Microbiology Difference Generally in virology naming and quantifying the organism suffices Occasionally drug resistance or genotype information needed for treatment. At the end of this you are the have the option to apply a predetermined treatment or stop pre-emptive treatment or not to treat (if no drugs available). In bacteriology namely the organism is only half the story There are different subtypes within an organism and some are more clinically relevant that others. Identifying susceptibility to antibiotics is one of the most significant components of diagnosis. Different species within an organism have evolved different molecular mechanisms to evade antibiotic pressure

24 Bacterial resistance strategies Bacterial have evolved four major bacterial resistance strategies: Preventing antimicrobials from reaching its target by reducing its ability to penetrate into the cell Excluding the antimicrobial agents from the cell via efflux pumps Inactivating of antimicrobial agents by modification or degradation Modifying the antimicrobial target within the bacteria

25 Molecular mechanisms of resistance These bacterial antibiotic resistance strategies are Genetically encoded Intrinsic resistance - resistance which is naturally coded and expressed by all (or almost all) strains of a particular bacterial species. Acquired resistance - changes in bacterial genome through mutation or horizontal gene acquisition which is limited to selected isolates of that particular species or group of microorganisms E.g. Mutation (MTB rifamycins); Horizontal gene transfer -Staph aureus resistance to methicillin (MRSA) All this complex information is easily examined observing the bacterial growth around discs of antibiotics. It is not easy to identify these by rapid NAAT genetic analysis.

26 Detecting Antimicrobial Resistance There are several antimicrobial susceptibility testing methods devoled including Dilution (broth and agar dilution method) Disk-diffusion E-test Automated methods NAAT testing PCR +/- DNA hybridization Each one has their respective advantages and disadvantages

27 Method Selection Selection of the appropriate method depends on the intended degree of accuracy convenience urgency availability of resources Cost Most commonly used methods are the agar disk-diffusion and the broth microdilution methods By comparison NAAT detection of antibiotic resistance is limited to specific targets.

28 Can NAAT completely replace routine culture and sensitivity? No Most microbes grow & multiply very quickly It is impossible to completely replicate culture cost-effectiveness (price and turnaround time) Applying NAAT to gather the same info on ID and resistance would require The use whole genome sequencing approach (antibiotic pumps) Full bioinformatics support and expertise Heavy reliance on computation data to link genomics to phenotype Gene may be present but not phenotypically expressed If this is applied to every clinical sample the whole computational biology will fall apart within a few minutes. The information delivered to the clinician at the end of this process would not be different to the one that you can get with simple antibiotic disc plate.

29 Automation and Bacteriology services Total Lab automation is having major impact on the delivery of Bacteriology services triggered by: Availability of MALDI-TOF MS (rapid ID) Laboratory consolidation Reports indicate that Lab automation has improved TAT and decreased hands-on plating time Decrease in TAT for Positive blood cultures identification has been reported to lead to earlier antibiotics therapy in 12% cases TAT for Urine result decreased from 24 hours to 16 hours Increase in the number of samples per staff (from to 2.6-fold) BD Kiestra TLA COPAN WASPLab

30 NAAT testing in Bacteriology service Molecular diagnostics techniques are currently widely used in Bacteriology. Slow and fastidious growing organisms, slow phenotypic susceptibility, (e.g. MTB takes 6 w) Clinical service has to wait weeks for an answer / treat empirically. Unknown organisms in aseptic fluids (16s/18s) Combined with other tests in the diagnostic algorithm (e.g. C. difficile, C. difficile PCR ribotyping ) Rapid detection of antibiotic resistance (e.g. meca- & mecc in MRSA, rpob gene MTB rifampicin resistance,) Panel-based molecular diagnostics in acute setting (e.g. acute gastroenteritis pathogens in stool, in CSF acute meningitis and encephalitis) GUM Screening programmes E.g. Neisseria gonorrhoea (NG) and Chlamydia trachomatis (CT) Infection Control and Hospital Epidemiology Improve standards of care / isolation

31 Application of NAAT on primary specimen NAAT when applied to primary specimens may show superior sensitivity and specificity on one specimen compared to another. E.g. MTB NAAT testing is superior when applied to respiratory specimens compared to other sites (98% on sputum smear positive and 73% of smear negative) However, in this example it is appropriate to use MTB NAAT testing in a less sensitive setting in order to diagnose rapidly tuberculus meningitis A positive NAAT results is often used as a rule-in mechanism but a negative results would not rule-out a diagnosis.

32 Infection control - a question of resources For the common organisms such as E. coli, staphylococci there is treatment available but there the question is how to prevent the spread of these bacteria and hospital acquired infection. At any time most hospitals would have 5% and 20% side rooms available for cases associated e.g. Vomiting and diarrhoea (due mainly to viral infections) cases associated with MRSA Multiresistant Gram-negative bacilli. Tuberculosis Rif resistant The question there is who deserves to go into the side rooms and who does not, considering the constraints within a hospital NAAT testing can provide sufficient information for rapid infection control assessment rule-in

33 Panel based molecular diagnostics Several tests have been designed for testing Positive blood culture bottles Stool - acute gastrointestinal pathogens Respiratory specimens acute respiratory pathogens Cerebrospinal fluid for - acute central nervous system infecton

34 Panel based approach (standard NAAT technology) Respiratory infections Respiratory Panel: FluA, B, FluA (H1N1), CMV, Pneumocystis jirovecii, H.influenzae type B, Bordetella spp., Moraxella catarrhalis, Klebsiella pneumoniae, Legionella spp., Salmonella spp. Bacterial pneumonia: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella spp. Gastroenteritis Viral: norovirus G1, G2, astrovirus, rotavirus, adenovirus, sapovirus Bacterial: Salmonella spp., Shigella spp., Yersinia enterocolitica, C difficile, Campylobacter coli/jejuni, VTEC Parasites: Entamoeba histolytica, Cryptosporidium spp., Giardia lamblia Meningitis Viral: herpes simplex virus 1, 2, varicella-zoster virus, enterovirus, mumps virus, parechovirus Bacterial: Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae (+/- group B Streptococcus (S. agalactiae), Listeria monocytogenes, Escherichia coli)

35 Blood culture Panel FilmArray 12h culture +TAT 1h Gram-positive bacteria Gram-negative bacteria Candida species Staphylococcus species Klebsiella oxytoca Candida albicans Staphylococcus aureus Klebsiella pneumoniae Candida glabrata Streptococcus species Serratia species Candida krusei Streptococcus agalactiae Proteus species Candida parapsilosis Streptococcus pyogenes Acinetobacter baumannii Candida tropicalis Streptococcus pneumoniae Enterococcus species Listeria monocytogenes Resistance genes meca; vana/vanb Haemophilus influenzae Neisseria meningitidis Pseudomonas aeruginosa Enterobacteriaceae Escherichia coli Enterobacter cloacae complex Resistance genes blakpc Verigene 12h culture +Tat 2.5H Gram-positive bacteria Staphylococcus aureus Staphylococcus epidermidis Staphylococcus lugdunensis Gram-negative bacteria Escherichia coli Klebsiella pneumoniae Klebsiella oxytoca Streptococcus anginosus group Pseudomonas aeruginosa Streptococcus agalactiae Acinetobacter species Streptococcus pneumoniae Citrobacter species Streptococcus pyogenes Enterobacter species Enterococcus faecalis Proteus species Staphylococcus species Streptococcus species Listeria species Resistance genes Resistance genes meca; vana/vanb blandm, blakpc, blaoxz, blavim, blactx-m

36 Sepsis - Direct Blood Detection IRIDICA BAC BSI Assay (8h) Identifying hundreds of diverse organisms by Performing multiple bacterial gene PCR amplification Fractionating the products using electrospray ionization mass spectrometry (PCR/ESI-MS) Analysing the PCR product ATGC content against a bacterial database. In a recent study (Metzgar D et.al. 2016; PLoS ONE 11(7): e _ Matched 80% of culture They could not determine antibiotic resistance phenotypes (limited to few broad spectrum) Should be considered an additional tool in the diagnostic regime

37 LOOKING AHEAD Ultimately all decisions in the future will be based on Health Economics Next Generation Sequencing (NGS) Use in Lab diagnostics will require Validated diagnostic kits Automated preparation solutions Bespoke bioinformatic solutions for each test (black box) Simple interpretative reporting Significant secure computer infrastructure and support.

38 Application of NGS Targeted NGS assays HIV-1 resistance sequencing (currently) MTB Due to cost of current Sanger sequencing. NGS can achieve the same TAT screening multiple samples at the same time Resistance prediction with high sensitivity and specificity (Requires established genotypic/phenotypic databases) Rapid identification of transmission chains For all Novel tests Pathway Health Economic analysis will be key for expensive testing strategies in order to offset test costs against overall savings

39 Whole Genome Sequencing Outbreak Breakthrough Year Microorganism Location 2008 Arenavirus Australia Mycobacterium tuberculosis Canada 2009 Methicillin-resistant Staphylococcus aureus (MRSA) United Kingdom 2009 Bas-Congo virus Democratic Republic of the Congo 2009 Influenza A virus H1N1 Worldwide Vibrio cholerae O1 biovar El Tor Haiti 2011 Carbapenem-resistant Klebsiella pneumoniae USA 2011 Escherichia coli O104:H4 Germany 2013 Clostridium difficile Worldwide 2013 Legionella pneumophila serogroup 1 United Kingdom 2015 Carbapenem-resistant Klebsiella pneumoniae Canada

40 Point of Care POC should provide an accurate and rapid answer to a limited number of clinical virology and microbiology questions and have a clear impact on patient management. POC assays address specific questions the requirements to hospitalize patients, to isolate contagious individuals, to initiate and focus anti-infective therapy Bacteria: Bordetella pertussis, C. difficile, Neisseria meningitidis, Streptococcus pneumoniae and S. pyogenes viruses (including) adenoviruses, dengue virus, enteroviruses and influenza viruses Parasites - P. falciparum.

41 Advances in molecular technology Miniaturization and simplification of highly complex molecular procedures are now extending the availability of molecular diagnostics particularly with POC devices The field of nanotechnology is growing by leaps and bounds and is aggressively applied to molecular diagnostics Simpler molecular platforms are promised by advances in microelectronics, microfluidics, and microfabrication Cost of new tests, improvements on TAT and effectiveness on early diagnosis will be key for their adoption. Return on investment for the clinical service is key

42 Thank You Your are showing me a Ferrari when I can only afford a Fiat Punto