The National Center for Biotechnology Information (NCBI) Pathogen A...

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The NCBI Pathogen Analysis Pipeline
to Support
Real Time Sequencing of Foodborne Pathogens
William Klimke
GMI9

NCBI Pathogen Detection Pipeline
NCBISubmissionPortal
BioSamples
SRA
GenBank
BioProject
NCBI Pathogen Pipeline
Kmer analys...

sample_name
organism
strain/isolate
Category (attribute_package)
1a) Clinical/Host-associated
1a1) specific_host
1a2) isol...

NCBI Pathogen Detection Pipeline
Submissions (Jan – May, 2016)

Automated Bacterial Assembly
SRA Reads sample 1
Trim reads
(Ns, adaptor)
Reference
Distance tree
Find closest reference ge...

1. Initial partition of isolates within each species by kmer distances
2. Within each partition, blast comparison of all p...

High SNP density
Cumulative count of differences
Iterative density filtering (Richa Agarwala modification of
Science. 2011...

Type Total targets in k-
mer tree
Targets in clusters (single linkage
<= 50 SNPs)
Salmonella 45297 38794
Listeria 9621 813...

http://www.ncbi.nlm.nih.gov/pathogens/
Results Available Now

there are several rows as NULL – means the target
either is not in a cluster (check last column) or is in a cluster
withou...

NCBI Pathogen Detection SNP Pipeline: example 1 - stone fruit outbreak

http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6410a6.htm?s_cid=mm6410a6_e#Fig
similar results to CDC wgMLST

MN chicken kiev outbreak
NCBI Pathogen Detection SNP Pipeline: example 2 – chicken kiev outbreak

NCBI Pathogen Detection SNP Pipeline Web viewer (coming soon):
example 3 – Elizabethkingia outbreak

wgMLST approach
• Complementary to SNP analysis e.g. consistency check
• Efficient for initial clustering of all isolates ...

• Fast & relatively simple
• Epidemiologists are
familiar with it
• Good for initial clustering
• Different heuristics
• C...

NCBI’s Role in Combating Antibiotic Resistant
Bacteria
“Create a repository of resistant bacterial
strains (an “isolate ba...

AMR efforts at NCBI
• With collaborators, build database of sequenced isolates with standardized
AMR metadata (i.e. accept...

Antibiogram Fields
• Fields designed to find balance between comprehensiveness and ease of
submission
• Data dictionaries ...

mcr-1 encoding organisms Total
E. coli 11
Salmonella 10
Antibiotic resistance

NCBI Outputs
Kmer tree
ftp://ftp.ncbi.nlm.nih.gov/pathogen/Results/
• Genome Workbench
• full SNP reports
• Integrated web...

Acknowledgements
Richa Agarwala
Azat Badretdin
Slava Brover
Joshua Cherry
Vyacheslav
Chetvernin
Robert Cohen
Michael DiCuc...

The National Center for Biotechnology Information (NCBI) Pathogen Analysis Pipeline to Support Real Time Sequencing of Foo...

The National Center for Biotechnology Information (NCBI) Pathogen Analysis Pipeline to Support Real Time Sequencing of Foo...

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