The pathogenic intestinal spirochaete Brachyspira pilosicoli forms a diverse recombinant species demonstrating some local clustering of related strains and potential for zoonotic spread

Background: Brachyspira pilosicoli is an anaerobic spirochaete that can colonizes the large intestine of many host species. Infection is particularly problematic in pigs and adult poultry, causing colitis and diarrhea, but it is also known to result in clinical problems in human beings. Despite the economic importance of the spirochaete as an animal pathogen, and its potential as a zoonotic agent, it has not received extensive study. 
Methods: A multilocus sequence typing (MLST) method based on the scheme used for other Brachyspira species was applied to 131 B. pilosicoli isolates originating from different host species and geographical areas. A variety of phylogenetic trees were constructed and analyzed to help understand the data. 
Results: The isolates were highly diverse, with 127 sequence types and 123 amino acid types being identified. Large numbers (50-112) of alleles were present at each locus, with all loci being highly polymorphic. The results of Shimodaira-Hasegawa tests identified extensive genetic recombination, although the calculated standardized index of association value (0.1568; P <0.0005) suggested the existence of some clonality. Strains from different host species and geographical origins generally were widely distributed throughout the population, although in nine of the ten cases where small clusters of related isolates occurred these were from the same geographical areas or farms/communities, and from the same species of origin. An exception to the latter was a cluster of Australian isolates originating from pigs, chickens and a human being, suggesting the likelihood of relatively recent transmission of members of this clonal group between species. 
Conclusions: The strongly recombinant population structure of B. pilosicoli contrasts to the more highly clonal population structures of the related species Brachyspira hyodysenteriae and Brachyspira intermedia, both of which are specialized enteric pathogens of pigs and poultry. The genomic plasticity of B. pilosicoli may help to explain why it has been able to adapt to colonize the large intestines of a wider range of hosts compared to other Brachyspira species. The identification of a clonal group of isolates that had been recovered from different host species, including a human being, suggests that zoonotic transmission by B. pilosicoli may occur in nature. Evidence for local transmission between the same host species also was obtained.