Enhancing Public Health Infectious Disease Genomics through Cloud Computing


Kelsey Florek, PhD, MPH
Senior Genomics and Data Scientist
Wisconsin State Laboratory of Hygiene
February 22, 2023

Slides live at:
www.k-florek.net/talks

@kflorek@mstdn.science
@kelsey_florek

Supported By

AWS Diagnostic Development Initiative (DDI)

Next Generation Sequencing

What is Next Generation Sequencing?

Sanger Sequencing

Next Generation Sequencing (Illumina)

Increases in data requires advanced analyses (MiSeq)

  • 15,000,000,000 ATGC's generated per sequencing run
  • 40,000 - 150,000 words in a novel
  • average word length in English is 4.79
  • one sequencing run would generate 32,963 novels with 95,000 words each

Increases in data requires advanced analyses (Nextseq 2000)

  • 360,000,000,000 ATGC's generated per sequencing run
  • 40,000 - 150,000 words in a novel
  • average word length in English is 4.79
  • one sequencing run would generate 791,121 novels with 95,000 words each

Genomics and Public Health Infectious Diseases

Public Health Aspects of Infectious Disease

  • Pathogen Surveillance
    • pathogen trends
    • priority setting
    • early warning system
  • Outbreak Investigations
    • source identification
    • risk assessments
    • prevent spread

Pathogen Surveillance: SARS-CoV-2

SARS-CoV-2 Wastewater

SARS-CoV-2 Clinical

SARS-CoV-2 Variant Waves in WI

SARS-CoV-2 Variant Waves in WI

Outbreak Investigation:
Drug Resistant Acinetobacter baumannii

Outbreak Initial Case

  • Patient at facility A with a lower respiratory infection 3 months after a heart transplant
  • Respiratory cultures revealed a carbapenem resistant A. baumannii
  • Treatment:
    • Polymixin-B
    • Meropenem
    • Colistin
    • Cefiderocol as compassionate treatment
  • Patient passed away, unclear if cause was sepsis
  • 5 additional patients from Facility A had sputum cultures that were positive for carbapenem resistant A. baumannii
  • Wisconsin State Laboratory of Hygiene

Antimicrobial susceptibility

  • Amikacin: Resistant
  • Aztreonam: Resistant
  • Cefepime: Resistant
  • Cefotaxime: Resistant
  • Ceftazidime: Resistant
  • Ciprofloxacin: Resistant
  • Colistin: Susceptible
  • Doripenem: Resistant
  • Doxycycline: Resistant
  • Gentamicin: Resistant
  • Imipenem: Resistant
  • Levofloxacin: Resistant
  • Meropenem: Resistant
  • Minocycline: Intermediate
  • Piperacillin-tazobactam: Resistant
  • Polymyxin-B: Susceptible
  • Ticarcillin-clavulanate: Resistant
  • Tobramycin: Resistant
  • Trimethoprim-sulfamethoxazole: Resistant

Case Definitions

  • Probable

    • Carbapenem resistant A. baumannii clinical isolate with outbreak AST profile
  • Confirmed

    • Carbapenem resistant A. baumannii clinical isolate genetically clustering with other outbreak isolates and harboring the OXA-24/40-like β-lactamase OXA-72

Case Definitions

  • Probable (n=43)

    • Carbapenem resistant A. baumannii clinical isolate with outbreak AST profile
  • Confirmed (n=22)

    • Carbapenem resistant A. baumannii clinical isolate genetically clustering with other outbreak isolates and harboring the OXA-24/40-like β-lactamase OXA-72

Summary

  • Next Generation Genomic Data is already large and growing with new technology
  • Critical reductions in time to result with genomic data to better inform public health policy and interventions
  • Infrastructure needs flexibility to adapt to changes in demand with the potential for high demand
  • Genomic data is a unique data type that doesn't fit with typical data solutions

Cloud Approaches to Bioinformatics

Managing a growing data infrastructure

Bioinformatics Workflow

Nextflow

Sequencing Analysis Infrastructure

Sequencing Analysis Infrastructure

https://dataportal.slh.wisc.edu/

Easy Genomics

Easy Genomics

Whats next?

Pathogen Genomic Data Needs Context!

Connect data systems across Public Health
enabling near realtime insights on infectious diseases

Sequencing Data Infrastructure

Acknowledgments

Abigail Shockey, PhD
Christopher Jossart, MPH
Dustin Lyfoung, MS

Special Thanks