As part of the on-going rollout of WGS at PHE, we needed to know the MLST Sequence Type (ST) of the completed Salmonella reference genomes. However, this info was not that easy to come across either in the literature or the Salmonella MLSTdb. I deteremined the ST of these genomes by converting the completed sequence to paired fastqs using pIRS, the running the fastqs through an MLST pipeline developed at PHE, which is based on SRST.

Table 1: the ST of Salmonella enterica reference genomes, determined using a PHE pipeline based on SRST. Asterix denotes a single locus variant.

Unfortunately, the insert table plugin for wordpress doesn’t seem to be working, so here is a tab separated text version of the above. Not as easy on the eye but copy/paste-able and google-able.

CP001138 Agona str. SL483 13
AE017220 Choleraesuis SC-B67 *66
CP001144 Dublin str. CT_02021853 *10
AM933172 Enteritidis P125109 *11
AM933173 Gallinarum str 287/91 331
CP003047 Gallinarum/pullorum str. RKS5078 92
CP001120 Heidelberg *15
CP003416 Heidelberg str. B182 *15
CP004027 Javiana str. CFSAN001992 24
CP001113 Newport str. SL254 45
CP000026 Paratyphi A ATCC 9150 (SARB42) 85
FM200053 Paratyphi A str. AKU_12601 85
CP000886 Paratyphi B str. SPB7 (SGSC 4150) *307
CP000857 Paratyphi C strain RKS4594 114
CP001127 Schwarzengrund *322
AL513382 Typhi CT18 2
CP003278 typhi str. p-stx-12 *1
CP002099 Typhi str. Ty21a 1
AE014613 Typhi Ty2 1
AE006468 Typhimurium LT2 19
FQ312003 Typhimurium SL1344 *19
CP001363 Typhimurium str. 14028S 19
CP003386 typhimurium str. 798 NOVEL_allele.19/1
FN424405 Typhimurium str. D23580 313
CP002487 Typhimurium str. ST4/74 19
AP011957 Typhimurium str. T000240 19
CP002614 Typhimurium str. UK-1 19