Handyman, Expert or DIY? Jacob Moran-Gilad, MD MPH ESCAIDE 2015 - - PowerPoint PPT Presentation

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Handyman, Expert or DIY? Jacob Moran-Gilad, MD MPH ESCAIDE 2015 - - PowerPoint PPT Presentation

Sep 01, 2022 130 likes •653 views

Choosing the Right Tool for the Job Handyman, Expert or DIY? Jacob Moran-Gilad, MD MPH ESCAIDE 2015 Eurosurveillance Seminar, 12 Nov 2015 Choosing the right tool? first let s define the Job! Local / hospital Emergency situation Type

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Choosing the Right Tool for the Job – Handyman, Expert or DIY?

Jacob Moran-Gilad, MD MPH

ESCAIDE 2015 – Eurosurveillance Seminar, 12 Nov 2015

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Choosing the right tool? first let’s define the Job!

Type of organism Diversity / typeability Type of sample Type of setting Local / hospital NRC International Emergency situation ‘One-off’ / ad hoc Routine task Outbreak investigation Population study Research Microbiologist Epidemiologist Clinician

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What makes a Bacterial Typing Tool ‘Right’?

  • Typeability & Discriminatory power
  • Reproducibility & Stability over time
  • Cost effectiveness
  • Ease of adoption and use, Speed
  • Agreed nomenclature, harmonised results
  • Portability and accessibility
  • Scalability
  • Amenable to QC/QA
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Where does typing take place? All over!

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Shall we refine the question?

Choosing the Right (Bioinformatics) Tool for the Job?!

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What’s between typing and mobile phones?

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Microbiological challenges - Legionella pneumophila

  • A significant cause of waterborne infections
  • Explosive outbreaks, a ‘celebrity’ disease
  • Difficult to control, highly regulated
  • Heavy reliance on traditional methods
  • Clinical diagnostic challenges
  • Cluster investigation challenges
  • International networking paramount
  • Need to ‘personalise’ risk assessment
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Evolution of Lp typing – mAbs

  • C. Luck JMM 1995
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Evolution of Lp typing - RAPD

N.S. Bansal & F. McDonell JCM 1997

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Evolution of Lp typing - AFLP

N.K. Fry et al., CMI 2005

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Evolution of Lp typing - PFGE

  • H. Zhou et al., AEM 2010
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Evolution of Lp typing – The ‘EWGLI’ SBT

  • J. Moran-Gilad et al., CMI 2013

7 genes flaA, pilE, asd, mip, mompS, proA, neuA

ST1

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Evolution of Lp typing – MLVA-8

  • C. Pourcel et al., JCM 2007
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Evolution of Lp typing – Spoligotyping

Ginevra et al. JCM 2012

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Microbiological challenges - Acinetobacter spp.

  • A significant cause of healthcare-associated infections

worldwide

  • High morbidity and mortality
  • Difficult-to-treat – MDR / XDR / PR
  • Various syndromes; unpredictable clinical course
  • Traditional micro methods – limited
  • Complex hospital epidemiology
  • Suboptimal typing schemes
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Evolution of Ab typing – rep-PCR

100 90 80 70 60 50 40 30 20

1882 1963 4598 193 4871 1590 822 4620 4488 19606 377 406 1831 1832 1257 1893 1302 1329 172 4555 4523 439 1576 661 1982 4570 1278 1378 1869 1311 359 1818 1858 1404 1445 1958 586 849 292 446 59 320 230 504 5657 5897 5780 108 5587 5510 217 1985 559 647 409 534 42 4663 5862 6029

Rep- PCR Pattern 1 Rep- PCR Pattern 2 Rep- PCR Pattern 3 Other pattern s Other patters

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Evolution of Ab typing - AFLP

  • L. Dijkshoorn et al., JCM 1996
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Evolution of Ab typing - PFGE

  • H. Seifert et al., JCM 2005
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Evolution of Ab typing - MLVA

  • J. Turton et al., EJCMID 2009
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S.G. Bartual et al., JCM 2005

Evolution of Ab typing – MLST (Oxford)

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  • A. DiPopolo et al., CMI 2011

Evolution of Ab typing – MLST (Pasteur)

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Evolution of Ab typing – 3LT (Poor man’s MLST)

  • J. Turton et al., CMI 2007
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Evolution of Ab typing – MLST comparison

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Evolution of Ab typing – ‘Tower of Babylon’

  • R. Zarrilli et al. IJAA 2013
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Evolution of typing - NGS

  • S. Shokralla et al. Molecular Ecology 2012
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NGS - a Disruptive Technology

NGS Platforms Sample Processing Bioinformatics, IT infrastructure

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NGS Application in Public Health Micro

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Contribution of Eurosurveillance to the body of knowledge on WGS typing

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NGS Application for LD Investigation - England

  • S. Reuter et al. BMJ Open 2013
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NGS Application for LD Investigation – Australia

R.M.A Graham et al. Epidemiol Infect 2014

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NGS Application for LD Investigation - Canada

  • S. Levesque et al. PLOS One 2014
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NGS Application for Ab investigation

  • T. Lewis et al. J Hosp Infect 2010
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NGS Application for Ab investigation

S.J. Salipante et al. JCM 2015

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NGS Application in Public Health Micro

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Current cgMLST Schemes

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Development of cgMLST scheme for Lp

  • J. Moran-Gilad et al. Eurosurv 2015
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Development of cgMLST scheme for Lp

  • J. Moran-Gilad et al. Eurosurv 2015
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Development of cgMLST scheme for Lp

  • J. Moran-Gilad et al. Eurosurv 2015
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Development of cgMLST scheme for Lp

  • J. Moran-Gilad et al. Eurosurv 2015
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Development of cgMLST scheme for Lp

  • J. Moran-Gilad et al. Eurosurv 2015

1,518 / 1,623 core genes used

C H

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C H 282-1 (ST1) 283/285 (ST1) 284 (ST1) O N 286-1 (ST1) 286-2 (ST93) 286-1 (ST1) 286-2 (ST93) 283/285 (ST1) 283/285 (ST1) Triple Lp (including double ST1) infection stemming from cold water system feeding the filtrator and aerosolised via humidifier

cgMLST changes our understanding of epi

  • J. Moran-Gilad et al. Eurosurv 2015
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Acinetobacter baumannii cgMLST

  • M. Silva et al. ECCMID 2015
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Diagnostic hierarchy in the era of NGS is driven by bioinformatics C&C

Expert Handyman DIY

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Expert DIY Handyman

  • J. Moran-Gilad et al. BMC ID 2015
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Current Public Health Challenges for Choosing the Right (Bioinformatics) Tools

  • Adoption of cgMLST schemes as a standard tool and making

them publicly available and widely implemented

  • Continuously optimise cgMLST schemes (refined core genome,

backward compatibility, setting thresholds for interpretability)

  • Build capacity for add-on SNP-based analyses for enhanced

resolution (micro-evolution, tree directionality)

  • Ensure quality, validation and harmonisation of WGS typing

(create nomenclature, proficiency testing, reference materials)

  • IT Infrastructure, data integration, genome repositories
  • Human resource - Cloning of bioinformaticians?
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The ESGLI NGS WG

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  • Transferable pipelines to support routine NGS

implementation globally– diffuse from Experts to DIY’s

  • Metagenomic FW&E microbiology
  • Metagenomic clinical sample analysis
  • Exploit BIG data, machine learning, cloud computing for

real time global genomic epidemiology

  • Embrace, develop and train ‘Public Health Informatics’

as an allied discipline

Future Challenges for Developing the Right Tools

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  • Prof. Jacob Moran-Gilad

giladko@post.bgu.ac.il

THANK YOU