Usually, these types of tools are specific to an organism if you are not looking for a general annotation tool, like Prokka, which would likely annotate surface protein genes.

For E. coli there is

• SerotypeFinder: which requires assemblies https://cge.cbs.dtu.dk/services/SerotypeFinder/ (web service) https://bitbucket.org/genomicepidemiology/serotypefinder/src/master/ (code behind webservice)

• ABRicate which has two E. coli databases (EcOH and Ecoli VFdb) but requires assemblies: https://github.com/tseemann/abricate

• seq_typing: which can take either reads or assemblies and predict E coli O and H antigens: https://github.com/B-UMMI/seq_typing

• SRST2: same db's as Abricate, takes reads https://github.com/katholt/srst2#using-the-vfdb-virulence-factor-database-with-srst2

I'm sure there are more out there, but this is a good start.