TABLE 2.

Results of phenotype, species-specific PCRs, and partial 16S rRNA gene sequence analysis for identifying 43 Brachyspira spp. isolates from 23 chicken farms

Farm no.	Chicken age (wk)	Flock size	Housing type	Sample no.	Species identification by:
					Phenotypea	Species-specific PCRb	16S rRNA gene sequencingc
1	24	5,800	Floor housing	1	NId	B. pilosicoli	NDe
				2	NI	NI	B. pilosicoli
				3	NI	B. intermedia and B. pilosicoli	ND
				4	NI	B. pilosicoli	ND
2	40	17,000	Floor housing	5 and 6	NI	B. intermedia	ND
				7	NI	B. pilosicoli	ND
				8	B. murdochii	NI	“B. pulli”
3	28	25,500	Floor housing+i	9	NI	NI	“B. pulli”
				10	B. innocens	NI	NDg
				11	B. innocens	NI	“B. pulli”
				12	NI	NI	B. innocens/B. murdochii cluster
				13	B. innocens	NI	B. innocens/B. murdochii cluster
				14	NI	B. pilosicoli	ND
4	44	9,000	Floor housing+	15	“B. pulli”	B. intermedia and B. pilosicoli	ND
				16	NI	B. intermedia and B. pilosicoli	ND
				17	NI	B. intermedia	ND
				18	NI	B. pilosicoli	ND
				19	NI	B. pilosicoli and B. hyodysenteriae	B. pilosicolih
5	NAf	18,000	Floor housing	20	NI	NI	B. hyodysenteriae/B. intermedia cluster
				21	NI	B. intermedia and B. pilosicoli	ND
				22	NI	B. intermedia	ND
6	36	9,000	Floor housing	23	NI	B. intermedia	ND
				24	B. innocens	B. intermedia	ND
				25	B. murdochii	B. intermedia	ND
				26	B. pilosicoli	B. pilosicoli	ND
7	52	33,500	Floor housing	27	NI	NI	“B. pulli”
8	35	15,000	Cage	28	NI	B. intermedia	NI
9	28	23,000	Floor housing	29	“B. pulli”	B. pilosicoli	ND
10	60	19,000	Floor housing+	30	NI	B. pilosicoli	ND
11	68	8,000	Floor housing+	31	NI	B. intermedia	ND
12	36	12,550	Aviary	32	NI	NI	NDg
13	64	60,000	Aviary	33	B. murdochii	B. intermedia	ND
14	64	15,000	Floor housing	34	NI	B. intermedia	ND
15	NA	NA	Floor housing	35	B. murdochii	B. intermedia	ND
16	32	29,000	Cage	36	B. innocens	NI	B. innocens/B. murdochii cluster
17	NA	20,000	Floor housing	37	NI	NI	B. innocens/B. murdochii cluster
18	NA	24,000	Floor housing	38	B. innocens	B. intermedia	ND
19	80	19,000	Floor housing	39	B. innocens	B. intermedia	ND
20	NA	NA	Floor housing+	40	murdochii	B. pilosicoli	ND
21	44	12,000	Floor housing+	41	NI	NI	“B. pulli”
22	28	30,000	Floor housing	42	murdochii	NI	“B. pulli”
23	29	21,000	Floor housing+	43	NI	B. pilosicoli	ND

^aPhenotype identifications are based on hemolysis and biochemical analysis (Table 1).

^bIndividual species-specific PCRs for B. pilosicoli, B. intermedia, and B. hyodysenteriae.

^cOnly samples negative in the species-specific PCRs or positive in the B. hyodysenteriae PCR were subjected to partial 16S rRNA gene sequencing.

^dNI, not identified biochemically and/or by PCR, or no pure culture was available for biochemical identification.

^eND, not done.

^fNA, not available.

^gSamples 10 and 32 were not sequenced, because they were negative in the genus-specific PCR.

^hAlso positive in the supplementary B. hyodysenteriae tlyA PCR.

ⁱThe plus indicates floor housing with free-range access.