Protocol

Software tools are likely to be updated/improved as time passes, and the database against which sequences are checked will become more complete as laboratories contribute more and more complete sequences. Occasionally these updates will necessitate changes to this pipeline.

Currently the script salmonella_typing/tasks.py runs the validation procedure (this is planned to be more user-friendly, see https://github.com/MDU-PHL/salmonella_typing/issues/14). This script runs three processes:

• rebuilds the salmonella_typing container, pulling in tool/database updates
• runs tests on new salmonella_typing container to ensure it is working as expected
• runs the new-build salmonella_typing on the list of verification isolates (in salmonella_typing/validation/salmonella_serotyping_reverification_test_set.csv) to generate a validation report.
• validation report is reviewed and if appropriate any corrections are made, repeating the previews 3 steps.
• validation report is signed off by Senior Bioinformatician and Quality Control
• previous container is archived in /home/seq/MDU/CONTAINERS/SALMONELLA_TYPING/SISTRvX.X.X/salmonella_typing_YYYYMMDD.simg (where YYYYMMMDD is the date the container was built; and X.X.X specifies the SISTR version used in the container)
• new container is copied to /home/linuxbrew/singularity/images/salmonella_typing.simg to put it into production.

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Re-verification Isolates and their Serotypes

DummyID	Genoserotype	PTP_source	phenoserotype	subspecies	EdgeCases
2999-99901	Mississippi		Mississippi
2999-99902	Enteritidis		Dublin	enterica	Edge case
2999-99903	Hessarek	NSRN PTP	Hessarek
2999-99904	Richmond	NSRN PTP	Richmond
2999-99905	Wandsbek	NSRN PTP	Wandsbek	salamae
2999-99906	Mundonobo	NSRN PTP	Mundonobo
2999-99907	Poona	NSRN PTP	Poona
2999-99908	Derby	NSRN PTP	Derby
2999-99909	Javiana	NSRN PTP	Javiana
2999-99910	Saintpaul		Saintpaul
2999-99911	Dublin	SSI EQA-8 Cluster, 2017	Dublin
2999-99912	Enteritidis	SSI EQA-8 Cluster, 2017	Enteritidis
2999-99913	Infantis	WHO EQAS GFN	Infantis
2999-99914	Havana	WHO EQAS GFN	Havana
2999-99915	Rissen	WHO EQAS GFN	Rissen
2999-99916	Weltevreden	WHO EQAS GFN	Weltevreden
2999-99917	Schwarzengrund	WHO EQAS GFN	Schwarzengrund
2999-99918	Typhimurium	WHO EQAS GFN	Typhimurium
2999-99919	Kentucky	WHO EQAS GFN	Kentucky
2999-99920	Paratyphi B		Paratyphi B
2999-99921	I 4,[5],12:i:-		1,4,12:i:-
2999-99922	Paratyphi B var. Java		Paratyphi B var. Java
2999-99923	IIIb 61:l,v:z		IIIb 61:i:z	diarizonea
2999-99924	Bovismorbificans		Bovismorbificans
2999-99925	IIIa 1,13,23:z4,z23,z32:-		IIIa	arizonae	Edge case
2999-99926	Virchow		Virchow
2999-99927	Breda		Chailey	enterica	Edge case
2999-99928	Paratyphi B var. Java monophasic		Sofia	salamae	Edge case
2999-99929	Stanley		Stanley
2999-99930	Agona		Agona
2999-99931	Paratyphi A		Paratyphi A
2999-99932	Typhi		Typhi
2999-99933	VI 1,6,14,25:b :1,7		1,6,14,25:z10:1,7	indica	Edge case
2999-99934	IV 1,44:z4,z32:-		Lohbruegge	houtenae	Edge case
2999-99935	Typhimurium	MMS103 validation
2999-99936