You can have numbers of methods for identification of bacterial species. The methods are able to identify a particular species of bacteria based on their morphological, cultural, biochemical, metabolic, genetic, pathogenic or antigenic characteristics. You can get specific biochemical tests for identifications of different bacterial species. For example, the indole test can be used for identification of coliform bacterial species, such as E. coli and other coliforms. You can also used selective and differentiation media for identification of particular bacterial species. Good examples are mannitols salt agar media for selection of staphylococus aureus, and Mackonkey agar medium for selection and differentiation of E. coli and Salmonella species. In addition, you can look for commercially available kits for identification of your desired bacterial species based on any one of the above mentioned major microbial characteristics.
You can use Bergey's manual of determinative bacteriology for identification of bacteria as suggested by Alemu Tekewe or by genetic methods like 16S rRNA sequencing or by serotyping in case of Salmonella
it is easily to confirm both isolates biochemically either traditionally by IMViC test for both or API 20 E identification kits or automatically by vitek identification system.
you can use the amplification of invA gene that is specific to Salmonella. (see: ed-dra et al. 2017. Microbial Pathogenesis 105 (2017) 340-345. https://doi.org/10.1016/j.micpath.2017.02.042