Brachyspira intermedia strain diversity and relationships to the other indole-positive Brachyspira species

 The aims of this study were to use multilocus sequence typing (MLST) to (i) investigate the population structure, diversity and molecular epidemiology of the weakly haemolytic anaerobic intestinal spirochaete Brachyspira intermedia, and (ii) determine the relationship of the species to the other two indole-positive but strongly haemolytic Brachyspira species—B. hyodysenteriae and “B. suanatina”. Seventy-seven B. intermedia isolates from pigs and chickens were analysed, with the nucleotide sequences of seven conserved genomic loci examined for each. B. intermedia was genetically diverse, with the 77 isolates being divided into 71 sequence types (STs) and 64 amino acid types (AATs). Many distinct groups of B. intermedia isolates were identified, with some isolates being separated from others by large genetic distances. Although both pig and chicken isolates were found in most groups, suggesting that cross-species transmission of such isolates may occur, some isolates from pigs were located in small groups that did not include chicken isolates, and vice versa. Eight clonal complexes (Cc) of STs were identified by e-Burst analysis. The Ccs contained between 2 and 5 STs, and between 2 and 9 isolates. Five Ccs contained multiple isolates from the same farms, collected at the same time, indicating the existence of ongoing minor genetic change amongst isolates at the farm level. On the other hand, isolates with quite different STs also were found amongst multiple isolates collected from some farms. By comparison with the much more restricted diversity observed for 111 isolates of B. hyodysenteriae, and 4 isolates of “B. suanatina”, it is difficult to justify including all weakly haemolytic indole-positive Brachyspira isolates in the single species B. intermedia.