01/11/2017
1. Background
Diagnostics & Classification
- Scottish Government-funded
- RESAS RD2.1.4
- RESAS RD2.1.5
- Sonia Humphris
- Ian Toth
- Emma Campbell
SRE Taxonomy
- enterobacterial taxonomy is difficult to resolve, in general
Historical classification mostly phenotypic, polyphasic
- all SRE originally Erwinia (1950s - bucket classification)
- now three distinct genera (Erwinia, Dickeya, Pectobacterium)
- binomial nomenclature not designed for large amounts of genome data, or metadata curation
- old names hold over in literature, collections
- name discontinuities affect analyses, databases
- Czajkowski et al. (2015) Ann. Appl. Biol. doi:10.1111/aab.12166 - SRE diagnostics
Historical Taxonomy
- Erwinia revised ≈1953 (Pectobacterium), ≈2003-2005 (Dickeya)
- Gardan et al. (2003) Int. J. Sys. Microbiol. doi:10.1099/ijs.0.02423-0 - SRE reclassification
- Samson et al. (2005) Int. J. Sys. Microbiol. doi:10.1099/ijs.0.02791-0 - SRE reclassification
Taxonomy For Legislation and Policy
Easy to incorporate into legislation (binary classification)
- Assumes taxonomy is assigned precisely and correctly
- Assumes taxonomy is a proxy for risk
- Historical phenotypic classification is semi-arbitrary (≈binary tree)
- Is a species concept appropriate for bacteria? (No)
- Is disease risk only transferred parent to offspring? (No: HGT)
- Is there 1:1 mapping from genome/phenotype to disease? (No)
- Are all currently known bacteria correctly classified? (No)
- Toth et al. (2006) Ann. Rev. Phyto. doi:10.1146/annurev.phyto.44.070505.143444 - horizontal transfer of pathogenicity
- Deans et al. (2015) PLoS Biol. doi:10.1371/journal.pbio.1002033 - no 1:1 map from taxonomy to disease
- Pritchard et al (2015) Anal. Methods doi:10.1039/c5ay02550h: Bacterial pathogen classification for policy
2. pyani
pyani
pyanievolved from diagnostics work on Pectobacterium/Dickeya- computational tool for rapid calculation and analysis of average nucleotide identity (ANI)
- First release August 2015; Current release: v0.2.7 (Oct 2017)
- Public webpage: http://widdowquinn.github.io/pyani/
- Available as
Dockercontainer:docker run -v ${PWD}:/host_dir leightonpritchard/average_nucleotide_identity
pyani
python package and scripts for ANI
- available on
PyPIandDocker - ANIm, ANIb etc.
- calculates, visualises results
- parallelises under SGE/OGE
- Pritchard et al. (2015) Anal. Methods doi:10.1039/C5AY02550H -
pyaniused on SRE
pyani in the wild
Downloads
- Since 2015: 22117
- 2017: 12808
- September 2017: 2164
- Used at
LINBase: Life Identification Numbers, Virginia Tech.
Reclassification: Pectobacterium
- Faure et al. (2016) Int. J. Syst. Microbiol doi:10.1099/ijsem.0.001524 - Reclassification of P. wasabiae
3. Pba in Scotland
JHI Collections
JHI holds historical pathogen samples from 1950s onwards
- sequence historical samples
- sequence current/recent outbreak samples
- environmental variation
- historical changes (evolution, introduction events)
- recently won grant to sequence ≈100 historical Pba isolates
Sequenced ≈50 P. atrosepticum isolates from infections (2009-2015)
- sourced from SASA (Greig, Gerry)
- Illumina sequencing
prokka,roary,QUAST,parSNP
A note on information
Torsten Seeman: https://twitter.com/torstenseemann/status/922735299398008832
SNP distribution
SNPs widespread across all P. atrosepticum genomes
parSNP Clades
P. atrosepticum divisible into four clades
Clades contain isolates found outwith UK/EU (from GenBank)
Distribution
all four clades widespread, no obvious geographical pattern
Not variety-related. Coexistence? Separate introductions?
Pangenomes
≈15% of P. atrosepticum genes are 'accessory'
| type | range | count |
|---|---|---|
| core | [99,100] | 3191 |
| soft core | [95,99) | 695 |
| shell | [15,95) | 850 |
| cloud | [0,15) | 3766 |
Variation within and between Pba clades.
Accessory genes presence/absence
accessory gene tree not congruent with the SNP tree
Potential HGT between clades 1 & 2, and clades 3 & 4?
Further Work
- Sequence 100 historical Scottish/global Pba isolates for context
- Core genome/wgMLST phylogeny
- Detailed analysis of genome composition differences
- HGT detection
- Can we identify introductions?
Acknowledgements
- Gerry Saddler
- Greig Cahill
- Scottish Society for Crop Research