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denglab / SeqSero

Salmonella serotyping from genome sequencing data
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SeqSero2 mistyping of Enteritidis and Monophasic Typhimurium #17

Open Litrup opened 2 years ago

Litrup commented 2 years ago

seqsero_version_summary.xlsx

Hi We recently installed the SeqSero2 and are facing some mistakes from the predictions. Worst case is Enteritidis and Monophasic variant of Typhimurium. You can see in attached spreadsheet, same fastq files run in both versions. Version one predicts 9:g,m:- and version 2 predicts 2:g,m:- Also Regarding the monophasic which is predicted in version 2 with a second phase. Even if this is a classic ST34 and clusters in an outbreak with strains predicted monophasic by version 1. All discrepansies were confirmed phenotypically in our lab and version 1 is true. Strains 17, 19, 21 and 32 are the major issues. We went back to the old version now - this is just a warning that errors are occurring. BW

denglab commented 2 years ago

Hi,

Thanks for the message. Would you please provide accession numbers of your questionable genomes so we can trouble shoot?

From: Eva Litrup @.> Sent: Friday, July 1, 2022 7:24 AM To: denglab/SeqSero @.> Cc: Subscribed @.***> Subject: [denglab/SeqSero] SeqSero2 mistyping of Enteritidis and Monophasic Typhimurium (Issue #17)

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seqsero_version_summary.xlsxhttps://github.com/denglab/SeqSero/files/9028413/seqsero_version_summary.xlsx

Hi We recently installed the SeqSero2 and are facing some mistakes from the predictions. Worst case is Enteritidis and Monophasic variant of Typhimurium. You can see in attached spreadsheet, same fastq files run in both versions. Version one predicts 9:g,m:- and version 2 predicts 2:g,m:- Also Regarding the monophasic which is predicted in version 2 with a second phase. Even if this is a classic ST34 and clusters in an outbreak with strains predicted monophasic by version 1. All discrepansies were confirmed phenotypically in our lab and version 1 is true. Strains 17, 19, 21 and 32 are the major issues. We went back to the old version now - this is just a warning that errors are occurring. BW

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