Origins of type strains of species of Pasteurellaceae
Avibacterium paragallinarum: IPDH 2403 isolated by K.-H. Hinz in 1970/71 from coryza in N. Germany.    
Muribacter muris: J. J. Ackerman in 1979 from mouse in USA.
Rodentibacter pneumotropicus: M8.19.48 isolated by E. Jawetz probably in 1948 from mouse in USA.
Pasteurella dagmatis: S. D. Henriksen 953/90 before 1961, from human nose in Norway.
Pasteurella multocida: W-9217 before 1962 from pig in Canada.

One-strain species
The many problems have been described in the paper of Christensen et al. 2001.
Unfortunately the problem has increased tremendously since that paper was published. In IJSEM, the majority publications are one-strains species and even one-strain genera.
For different reasons we have been able to limit one-strain species and one-strain genera in the Pasteurellaceae.

Working with the Nagoya protocol
The protocol was implemented 12 October 2014. Meaning that only samples taken after this day are covered by the protocol.
The paper of Overmann & Scholz 2017 describes the implications with prokaryotic strains.
A point made in this paper is that most prokaryotes are globally distributed and that many of the concepts made in the Nagoya protocol are difficult to apply to microorganisms.  
DSMZ maintains a website for explaining the Nagoya protocol and answering difficult questions.