You can simply specify the database file name in the command line:

bash-3.2 # sqlite3 UserDb.sqlite
SQLite version 3.16.2 2017-01-06 16:32:41
Enter ".help" for usage hints.

sqlite> .databases
main: /db/UserDb.sqlite

sqlite> .tables
accountLevelSettings  genres               syncedThumbs
collectionActivity    recordingFilter      thumbs
contentStatus         syncedContentStatus 

sqlite> select count(*) from genres;
10

Moreover, you can execute your query from the command line:

bash-3.2 # sqlite3 UserDb.sqlite 'select count(*) from genres'
10

You could attach another database file from the SQLite shell:

sqlite> attach database 'RelDb.sqlite' as RelDb;

sqlite> .databases
main: /db/UserDb.sqlite
RelDb: /db/RelDb_1.sqlite

sqlite> .tables
RelDb.collectionRelationship  contentStatus               
RelDb.contentRelationship     genres                      
RelDb.leagueRelationship      recordingFilter             
RelDb.localizedString         syncedContentStatus         
accountLevelSettings          syncedThumbs                
collectionActivity            thumbs                      

The tables from this 2nd database will be accessible via prefix of the database:

sqlite> select count(*) from RelDb.localizedString;
2442

But who knows how to specify multiple database files from the command line to execute the query from the command line?