Over two thirds of bovine respiratory isolates (91 of 128) belong to just three STs (ST13, ST79 and ST80). All three of these STs included UK isolates, ST13 and ST80 included French isolates and 7 of 8 US cattle isolates were ST79 (the remaining US isolate was ST135, an SLV of ST79). Seven isolates from calves sampled as part of a cross-sectional study in Scotland in 2008, from 7 different farms, grouped into ST123, which was unrelated to any other ST found (using the NU7026 in vitro criterion of sharing 5 of 7 alleles). At the est locus, these isolates had a unique allele (allele est-50) which has a single nucleotide insertion, resulting in a frame shift mutation. The functional significance of this is unknown.

The majority of HS isolates (9 of 12; 7 cattle, 2 buffalo) belonged to a unique sequence type (ST122), which also included 2 elephant and one bison isolate of unspecified clinical status. The 28 ovine isolates grouped into 19 STs; no ST was found in both Spanish and New Zealand sheep, although multiple closely related STs (SLVs and DLVs) were identified across both groups (Figure 1). Seven porcine isolates were typed as ST13 and an additional 6 isolates belonged to 5 STs, with one ST (ST9) also

found in cattle, two STs that were DLVs of cattle-associated STs and 2 STs found in pigs only (Figure 1). Eight novel STs were detected in the eight avian isolates typed in the current study. Most STs were specific to host PF-4708671 chemical structure of origin (Figure 1), the exceptions being ST13 (40 bovine respiratory and 7 porcine isolates), ST122 (10 bovine HS and 2 elephant isolates), ST 132 (3 ovine and 1 bovine isolates) and ST9 (1 porcine, 1 bovine and 1 human isolate). A highly significant Standardised Index of Association (IS A) (0.45, P = 0.000) in cattle respiratory

isolates indicated the presence of linkage disequilibrium within this population of P. multocida isolates and the results of SplitsTree analysis corroborated this, showing a tree-like, rather than a network, structure (Additional file 1, Figure S1). Significant linkage disequilibrium was also detected when all 195 isolates were analysed (IS A = 0.33, P = 0.000) Obeticholic Acid ic50 and a tree-like structure was again observed on split decomposition analysis (Additional file 2, Figure S2). In the absence of strong evidence for recombination, a Neighbour-Joining tree was constructed from concatenated sequences (Figure 2). The population structure as demonstrated by eBURST analysis was generally maintained, with some substructuring within populations associated with specific niches, for example within ovine and bovine respiratory isolates. Bovine respiratory isolates identified as CC13 MCC950 mouse formed a discrete cluster with the inclusion of ST88, which is a DLV of STs 79 and 80; no bovine non-respiratory associated ST was related to this cluster (Figure 2).