Tracking infectious disease and drug resistance using whole genome sequencing


Richard Neher
Biozentrum, University of Basel


slides at neherlab.org/201902_lausanne_genomics_days.html

Sequences record the spread of pathogens

images by Trevor Bedford

Human seasonal influenza viruses

slide by Trevor Bedford


  • Influenza viruses evolve to avoid human immunity
  • Vaccines need frequent updates

nextstrain.org

joint project with Trevor Bedford & his lab

Enterovirus D68 -- with Robert Dyrdak, Emma Hodcroft & Jan Albert

  • Non-polio enterovirus
  • Almost everybody has antibodies against EV-D68
  • Large outbreak in 2014 with severe neurological symptoms in
    young children (acute flaccid myelitis)
  • Another outbreak in 2016
  • Outbreaks tend to start in late summer/fall
  • Several reports of EV-D68 outbreaks last fall
    (201 AFM cases in the US in 2018)

How does EV-D68 spread? Does it change?

nextstrain.org/enterovirus

joint work with Robert Dyrdak, Emma Hodcroft & Jan Albert

Whole genome deep sequencing of Enterovirus D68

  • Amplified in 4 overlapping segments
  • Illumina sequenced to high coverage
Dyrdak et al, biorxiv

iSNV frequency accuracy and sequencing errors

  • iSNV frequencies reproducible above 1%
  • background at around 1/1000
Dyrdak et al, biorxiv

Infections with multiple variants

  • A set of iSNVs at very similar frequencies in full linkage
  • Suggest infection with two related variants
  • 3 out of 50 samples: Implies high prevalence
Dyrdak et al, biorxiv

Carbapenemase producing bacteria

  • Reserve antibiotics used to treat MDR bacteria
  • Introduced in the 1980ies
  • Resistance spread rapidly
  • Resistance is mediated by several distinct beta-lactamases
    → pressing public health problem
    → fascinating instance of genes sweeping the globe by horizontal transfer

Tracking bacteria by sequencing

  • Illumina → millions of short reads (<500bp)
  • Too short to bridge repetitive elements
  • → assemblies are fragmented into 100s of "contigs"
  • Problem: all the important bits are flanked by repetitive/mobile elements

(really terrible example)

Images: illumina.com, github.com/rrwick

Long-read sequencing

Long-read sequencing of Carbapenemase producing bacteria

  • Contigs with drug resistance genes ~1-6 genes
    → no phylogenetic resolution
  • long-read assemblies give full length plasmids
  • tracking via synteny and structural diversity, not SNPs
    → we need to reconstruct spread from genome structure evolution
Noll et al, biorxiv, 2018

Synteny alignments of Carbapenemase containing loci

  • Structural changes resolve evolutionary relationships
  • Different KPC alleles are found on the same backgrouond
  • Identical KPC alleles are found on different backgrounds
  • Similar plasmids are spread across MLSTs and species boundaries
Noll et al, biorxiv, 2018

Synteny alignments of Carbapenemase containing loci

Noll et al, biorxiv, 2018

Summary

  • Timely data sharing + automated analysis allows near real-time tracking of influenza
  • Such analyses provide important input for vaccine strain selection
  • Sequencing, analysis, and dissemination can be rapidly set-up for emerging pathogens
  • Bacterial pathogens come with a special set of challenges
  • Fascinating instance of evolution beyond SNPs

Acknowledgments -- nextstrain

  • Trevor Bedford
  • Colin Megill
  • Pavel Sagulenko
  • Sidney Bell
  • James Hadfield
  • Wei Ding
  • Emma Hodcroft
  • Sanda Dejanic
  • John Huddleston
  • Barney Potter

Acknowledgments -- Enterovirus

  • Robert Dyrdak
  • Jan Albert
  • Lina Thebo
  • Emma Hodcroft
  • Bert Niesters (Groningen)
  • Randy Poelman (Groningen)
  • Elke Wollants (Leuven)

Acknowledgments -- Bacteria

  • Wei Ding
  • Nicholas Noll
  • Eric Ulrich
  • Adrian Egli (at USB)

With-in host diversity

  • Above 0.5%, iSNVs are biological
  • Most samples have few iSNVs, three had more than 20
Dyrdak et al, biorxiv