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1.1.3

Serovar nomenclature update after USA Cantaloupe Outbreaks in November 2023. The O24 and O25 antigens would not be wet-lab typed reliably causing the collapse of certain serovar pairs detailed below (Table 1). The selected serovar in the pair is the one that will be reported by SISTR and the other serovar in the pair will be dropped. No O24 or O25 will be reported in the antigenic formula (Table 2).

Table 1 - serovar pairs that were collapsed

Serovar pair Serovar selected in v1.1.3
Soahanina - Sundsvall Sundsvall
Martonos - Finkenwerder Finkenwerder
Midway - Florida Florida
Lindern - Charity Charity
Bahrenfeld - Onderstepoort Onderstepoort
Schalkwijk - Moussoro Schalkwijk
Amberg - Boecker Boecker
Carrau - Madelia Carrau
Chichiri - Uzaramo Uzaramo
Poano - Stafford Poano

Changes of serovar assignments in sistr/data/genomes-to-serovar.txt file

The following updates were done to better reflect the O24 and O25 nomenclature together with updated Paratyphi B and Paratyphi B var. Java few genome designations with correct variant assignments

genome accession serovar previous serovar current
SAL_DA9822AA Soahanina Sundsvall
SRR1815423 Soahanina Sundsvall
SRR2889947 Soahanina Sundsvall
SRR2889992 Soahanina Sundsvall
SRR3996854 Soahanina Sundsvall
SRR3669910 Soahanina Sundsvall
SRR3732330 Soahanina Sundsvall
SRR3713652 Soahanina Sundsvall
SRR3713653 Soahanina Sundsvall
SRR3978444 Soahanina Sundsvall
SRR2011392 Soahanina Sundsvall
SRR1068363 Soahanina Sundsvall
ERR161888 Soahanina Sundsvall
SAL_BA5034AA Soahanina Sundsvall
SAL_EA3233AA Soahanina Sundsvall
SAL_GA9094AA Soahanina Sundsvall
SRR1158155 Soahanina Sundsvall
SRR2751907 Soahanina Sundsvall
SRR4237685 Soahanina Sundsvall
SRR5010548 Soahanina Sundsvall
09_6055 Madelia Carrau
11_0879 Madelia Carrau
SAL_BA1830AA Madelia Carrau
SAL_CA7979AA Madelia Carrau
SAL_DA4289AA Madelia Carrau
SAL_DA7475AA Madelia Carrau
SAL_EA4948AA Madelia Carrau
SAL_FA5821AA Madelia Carrau
SAL_HA4780AA Madelia Carrau
SAL_HA4886AA Madelia Carrau
SRR1269415 Madelia Carrau
SRR1548430 Madelia Carrau
SRR1805645 Madelia Carrau
SRR2104612 Madelia Carrau
SRR2911800 Madelia Carrau
SRR3933147 Madelia Carrau
SRR4098716 Madelia Carrau
SRR1258654 Madelia Carrau
SRR1582141 Madelia Carrau
SRR4019409 Madelia Carrau
SRR4244476 Madelia Carrau
SRR2075023 Madelia Carrau
SRR5132365 Madelia Carrau
SRR5051381 Madelia Carrau
SRR3743984 Madelia Carrau
SRR5054238 Madelia Carrau
SRR3928735 Madelia Carrau
SRR1586586 Madelia Carrau
SRR2976043 Madelia Carrau
SRR2962333 Madelia Carrau
SRR3928732 Madelia Carrau
SRR3928736 Madelia Carrau
SRR2962332 Madelia Carrau
SAL_EA2874AA Bahrenfeld Onderstepoort
SAL_FA0525AA Bahrenfeld Onderstepoort
SRR3173783 Bahrenfeld Onderstepoort
SAL_DA7014AA Martonos Finkenwerder
SRR1300569 Martonos Finkenwerder
SRR1973814 Martonos Finkenwerder
17-2557 Paratyphi B var. Java Paratyphi B
17-8544 Paratyphi B var. Java Paratyphi B
17-9304 Paratyphi B var. Java Paratyphi B
18-0116 Paratyphi B var. Java Paratyphi B
17-7324 Paratyphi B var. Java Paratyphi B
17-9312 Paratyphi B var. Java Paratyphi B

Changes to Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv antigen to serovar lookup database

Removed the following entries

  1. Martonos,"6,14,24",d,"1,5",,H,FALSE,enterica
  2. Midway,"6,14,24",d,"1,7",,H,FALSE,enterica
  3. Lindern,"6,14,[24]",d,"e,n,x",,H,FALSE,enterica
  4. Bahrenfeld,"6,14,[24]","e,h","1,5",,H,FALSE,enterica
  5. Moussoro,"1,6,14,25",i,"e,n,z15",,H,FALSE,enterica
  6. Amberg,"6,14,24","l,v","1,7",,H,FALSE,enterica
  7. Madelia,"1,6,14,25",y,"1,7",,H,FALSE,enterica
  8. Soahanina,"6,14,24",z,"e,n,x",,H,FALSE,enterica
  9. Chichiri,"6,14,24","z4,z24",-,,H,TRUE,enterica
  10. II 4:a:z39,"1,4,12,[27]",a,z39,,B,FALSE,salamae

The following entries were modified in the in the O_antigen field as such

Table 2 - updated antigenic formulas for the O24-25 serovars

Before After (SISTR v1.1.3)
Sundsvall,"[1],6,14,[25]",z,"e,n,x",,H,FALSE,enterica Sundsvall,"6,14",z,"e,n,x",,H,FALSE,enterica
Finkenwerder,"[1],6,14,[25]",d,"1,5",,H,FALSE,enterica Finkenwerder,"6,14",d,"1,5",,H,FALSE,enterica
Florida,"[1],6,14,[25]",d,"1,7",,H,FALSE,enterica Florida,"6,14",d,"1,7",,H,FALSE,enterica
Charity,"[1],6,14,[25]",d,"e,n,x",,H,FALSE,enterica Charity,"6,14",d,"e,n,x",,H,FALSE,enterica
Onderstepoort,"1,6,14,[25]","e,h","1,5",,H,FALSE,enterica Onderstepoort,"6,14","e,h","1,5",,H,FALSE,enterica
Schalkwijk,"6,14,[24]",i,"e,n,z15",,H,FALSE,enterica Schalkwijk,"6,14",i,"e,n,z15",,H,FALSE,enterica
Boecker,"[1],6,14,[25]","l,v","1,7",,H,FALSE,enterica Boecker,"6,14","l,v","1,7",,H,FALSE,enterica
Carrau,"6,14,[24]",y,"1,7",,H,FALSE,enterica Carrau,"6,14",y,"1,7",,H,FALSE,enterica
Uzaramo,"1,6,14,25","z4,z24",-,,H,TRUE,enterica Uzaramo,"6,14","z4,z24",-,,H,TRUE,enterica
Poano,"[1],6,14,[25]",z,"l,z13,z28",,H,FALSE,enterica Poano,"6,14",z,"l,z13,z28",,H,FALSE,enterica

New output field antigenic_formula

  • Added antigenic_formula field that aggregates the O, H1 and H2 antigen values in a single location for convenience

New argument --list-of-serovars

  • Added --list-of-serovars option allowing user to provide a single column text file listing all serovars of interest to match against the SISTR prediction. The result will be reported in predicted_serovar_in_list field as Y or N if there is match or otherwise. This could be useful for cases when only a certain list of serovars could be reported

New d-tartrate message for Paratyphi B, Paratyphi B var. Java andI 1,4,[5],12:i:- serovars

  • If Paratyphi B and Paratyphi B var. Java serovar is predicted and the --qc is selected, the following message will appear in qc_messages field Perform d-tartrate test (dT) to differentiate between Paratyphi B and Paratyphi B var. Java. The dT+ result is indicative of variant Java.
  • If monophasic I 1,4,[5],12:i:- predicted, then the qc_messages field will suggest d-tartrate test via this message Perform d-tartrate test (dT) as both dT+ and dT- I 1,4,[5],12:i:- subtypes exist.

1.1.1

  • Fixed issue with sorting of BLAST results (causing cgMLST types to be different between BLAST versions). Pull request #43.

1.1.0

  • Significant updates to SISTR antigen biomarker and cgMLST database