Diagnosis of infectious diseases and confirmation of diagnosis. Molecular epidemiology of emerging/re-emerging pathogens

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1 LA PREPARAZIONE E LA RISPOSTA ALLE EMERGENZE INFETTIVE Padova, 20 settembre 2012 Laboratory advanced technologies in the support of Public Health interventions in infectious disease emergencies Prof. Giorgio Palù, M.D. Director, Department of Molecular Medicine, University of Padova Head, Clinical Microbiology and Virology, Padova University Hospital

2 THE ROLE OF A THIRD LEVEL REFERENCE CENTER (REGIONAL AND MACROREGIONAL DISTRICT) Diagnosis of infectious diseases and confirmation of diagnosis Diagnosis requiring special expertise and containment (BL3 or plus) Molecular epidemiology of emerging/re-emerging pathogens Genotypic-phenotypic dissection of microbial resistant traits Introduction and validation of innovative technologies Probing new guidelines in diagnostic procedures Role as a proponent of clinical protocols of therapy and prevention

3 OUTCOMES OF INFECTIOUS DISEASE SURVEILLANCE BY A THIRD LEVEL REFERENCE CENTER Best practice & appropriateness in the management of major issues in clinical and laboratory medicine Impact on costs of medicines, reagents, personnel and procedures Impact on public health control Scientific contributions Innovation, R&D, technology transfer, Intellectual property Collaboration with international, national and regional authorities

4 Clinical microbiology in the genomics era Technology evolution since the late 19 th century has lead to a great change in our understanding of microbiology today. Recognition of new microbial and viral species Whole sequencing of microbial genomes Metagenomics New diagnostic tools (MS, NGS, automation) Easier identification of microorganisms (e.g., MALDI-TOF) Multiplexing (e.g., multiplex PCR, microarray, 454 pyrosequencing) Real-time microbial genome sequencing (e.g., EHEC, WNV) Fast and sensitive antibiotic resistance testing (e.g., MALDI-TOF, NGS)

5 Padova Clinical Microbiology Lab Department of Molecular Medicine Clinical Microbiology & Virology

6 Microbiology and Virology Unit, Padova University Hospital Facilities and research activities BSL3 lab for virus isolation and culture MS and HPLC equipments for TDM State-of-the-art genomics and proteomics facilities. Bioinformatics expertise Tools for immunity testing Research activity molecular epidemiology and pathogenesis of infectious diseases, genomics of microorganisms and host, proteomics, antimicrobial drug resistance, antimicrobial drug-design, infection and immunity, new vaccine development, cell and gene therapy of infectious diseases and cancer.

7 The clinical microbiology lab Subspecialty Labs Conventional culture, identification, and isolation methods Antimicrobial susceptibility testing Molecular methods Automation Proteomics Genomics Emergency examinations

8 Quality management in microbiology Accreditation (ISO standard 15189) Quality management system Continual improvement Process approach

9 Process map for the clinical microbiology lab Guidelines, plans of action Patient Prescription Resources allocated Strategic and management process Organization management Collaboration, contracts Customer feedback, complaints Nonconformity management, corrective actions Evaluations (audits, indicators, mangement review) Pre-analytical phase sampling transport reception allocation dispatch to other labs storage Operational processes Analytical phase method validation and performace verification technical validation internal and external QC in-vitro medical device vigilance Human resource management Documentation management Equipment and reagent control IT resource management Hygiene, safety, premises and environment Technology review Sustainable development Continual improvement Post-analytical phase biological validation reporting invoicing storage of samples Record control, traceability, archiving Procurement Information Results Resource requirements Support processes

10 Implementation of NGS technology in the clinical microbiology and virology laboratory Diagnostic needs Research needs Skills in NGS protocols set up (wet lab team) NGS workflow NGS platform Analytical validation Clinical validation Skills in NGS data assembly and analysis (bioinformatic team) QA/QC Routine testing

11 NGS Platforms Roche/454 FLX: 2004 Illumina Solexa Genome Analyzer: 2006 Applied Biosystems SOLiD TM System: 2007 Helicos Heliscope TM : 2008 Pacific Biosciencies SMRT: 2010 Ion Torrent TM PGS: 2011 Oxford Nanopore Sequencing: 2012

12 Applications of advanced technologies by the Regional Reference Lab to support Public Health in infectious disease emergencies: Some examples.

13 Phenotypic and molecular characterization of MDR pathogens Hospital infections Antimicrobial susceptibility testing K. pneumoniae MDR MLST Antiviral drug resistance Whole genome sequencing New antimicrobial drug development

14 Preventing and monitoring carbapenemase spreading Ultra-rapid rapid detection of bla KPC1/ by real-time PCR from perirectal and nasal swabs New method: less than 2 hrs to detect KPC presence in easily available specimens high sensitivity (100%) and specificity (98%) Application: KPC surveillance and containment in ICU, surgical and medical wards 60 bp amplicon detection of bla KPC1/ Richter et al. JCM 2012

15 pkpn101-it, a novel fully sequenced bla KPC-2 plasmid, from an extremely drug-resistant resistant Klebsiella pneumoniae ST101 isolate Frasson et al. J Clin Microbiol 2012

16 Anti-Influenza Compounds that Act by a Novel Mechanism

17 Our Target: The Interaction between the PA and PB1 subunits of Flu RNA Polymerase Flu polymerase is composed of three subunits: PA, PB1, and PB2; their interactions are essential for virus replication In 2008, two crystal structures of the PA-PB1 binding interface have been published: both structures showed that the C-terminal domain of PA forms a highly hydrophobic groove into which the amino-terminal residues of PB1 can fit by forming an α-helix He et al., Nature 2008, 454: Obayashi et al., Nature 2008, 454:

18 New Compounds Acting on Flu Virus Polymerase The new compound PA PB1 PB2

19 N F O O O O O N NH 2 Cl H 2 N OO S NH N N F N + H N N O N N + O O

20 Surveillance for emerging infections and outbreaks N. meningitidis infection Influenza Measles West Nile virus disease Dengue and chikungunya Etc. Clinical microbiologists have the expertise necessary to handle the unexpected!