Salmonella Isolates and Serotyping

The analyses presented here are based on 4257 isolates whose data has been submitted to http://mlst.ucc.ie/mlst/dbs/Senterica by ourselves and others. Of these, 1770 are maintained in the strain collection of MA at University College Cork, and 1042 in the strain collection of FXW at the Institut Pasteur, for a total of 2643 in either or both of those collections. Biotyping and serotyping were performed in multiple laboratories but most of the tests were performed under the supervision of FXW or MC. Serotyping and biotyping were according to the modified Kauffmann-White scheme [2] , except as described below.
Basic information on all isolates can be downloaded from the website. In addition, a detailed description of strain properties for Paratyphi B and Java isolates is presented in Table S6. The distinction between Paratyphi B and Java was based on two tests, which gave concordant results after up to 7 days incubation: the lead acetate protocol 1 for d-tartrate fermentation described by Malorny et al. [58] (link) and the ability to grow on d-tartrate as the sole carbon source as described by Weill et al. [64] (link). The start codon of STM3356 was sequenced as described by Malorny et al. [58] (link).
Table S7 gives detailed information on results with 6,7:c:1,5 isolates. These were assigned to serovars on the basis of the biochemical properties which are summarized in Table 3, and which are similar to the tests and recommendations by Le Minor et al. [65] . Mucate utilization, ducitol fermentation and H₂S production were evaluated after 24 hrs incubation in standard media and tartrate fermentation was evaluated after 7 days, as described above.
A separate manuscript is in preparation on differences between the contents of Selander's SARA and SARB collections. The conclusions drawn here were largely based on isolates stored by Kenneth E. Sanderson and corroborated by the collection of Fidelma Boyd. Serovar assignments were according to information uploaded to the website except that many atypical isolates and the Paratyphi B, Java and 6,7:c:1,5 isolates were retyped.