Table 3.

Confirmation and identification of samples positive to either culture or screening tetraplex real-time PCR.

Product	From	Sample ID	Method useda	Resultsa,b	Identified as
Pasteurized whole milk	Cattle	1	ITS sequencinge	M. fortutitum str.: 86–97%, 96–100%	M. fortuitum complex
Whole milk powder	Cattle	2	ITS sequencingd	M. fortutitum str.: 99%, 97%	M. fortuitum complex
Pasteurized milk fresh cheese	Cattle	3	ITS sequencingd	M. terrae/M. arupense str.: 100%, 100%	M. terrae complex
Pasteurized milk fresh cheese	Cattle	4	ITS sequencingd	M. fortutitum str.: 100%, 100%	M. fortuitum complex
Pasteurized milk fresh cheese	Cattle	5	ITS sequencingd	M. gordonae str.: 96%, 98%	M. gordonae
Pasteurized milk fresh cheese	Cattle	6	ITS sequencingd	M. fortutitum str.: 99%, 100%	M. fortuitum complex
Pasteurized milk soft cheese	Cattle	7	ITS sequencingd	M. fortutitum str.: 100%, 100%	M. fortuitum complex
Pasteurized milk greek style yogurt	Cattle	8	ITS sequencingd	M. terrae/M. arupense str.: 100%, 100%	M. terrae complex
Mortadella cold cut	Pig	9c	ITS sequencinge	M. senegalense str.: 99%, 82%	M. fortuitum complex
Pasteurized whole milk	Cattle	10	IS screening	IS900+, ISMap02+, IS1245−, IS901−, FR300+	M. avium subsp. paratuberculosis
Powdered infant formula	Cattle	11	IS screening	IS900+, ISMap02+, IS1245−, IS901−, FR300+	M. avium subsp. paratuberculosis
Powdered infant formula	Cattle	12c	IS screening	IS900−, ISMap02−, IS1245+, IS901−, FR300+	M. avium subsp. hominissuis
UHT milk cream	Cattle	13	IS screening	IS900+, ISMap02+, IS1245−, IS901−, FR300+	M. avium subsp. paratuberculosis
Pasteurized milk fresh cheese	Cattle	14	IS screening	IS900+, ISMap02+, IS1245−, IS901−, FR300+	M. avium subsp. paratuberculosis
Pasteurized milk fresh cheese	Cattle	15	IS screening	IS900+, ISMap02+, IS1245−, IS901−, FR300+	M. avium subsp. paratuberculosis
Pasteurized milk fresh cheese	Cattle	16	IS screening	IS900+, ISMap02+, IS1245−, IS901−, FR300+	M. avium subsp. paratuberculosis
Ground meat	Cattle	17c	IS screening	IS900−, ISMap02−, IS1245+, IS901−, FR300+	M. avium subsp. hominissuis
Hamburger	Horse	18	IS screening	IS900−, ISMap02−, IS1245+, IS901−, FR300+	M. avium subsp. hominissuis
Fresh sausage	Chicken	19	IS screening	IS900−, ISMap02−, IS1245+, IS901−, FR300+	M. avium subsp. hominissuis
Fresh sausage	Chicken	20c	IS screening	IS900−, ISMap02−, IS1245+, IS901−, FR300−	M. avium subsp. avium
Whole milk powder	Cattle	21	RD screening	RD1+, RD4−, RD9−, RD12−	M. bovis
Powdered infant formula	Cattle	22	RD screening	RD1+, RD4−, RD9−, RD12−	M. bovis
Butter	Cattle	23	RD screening	RD1+, RD4−, RD9−, RD12−	M. bovis
Butter	Cattle	24	RD screening	RD1+, RD4−, RD9−, RD12−	M. bovis
Pasteurized milk fresh cheese	Cattle	25	RD screening	RD1+, RD4−, RD9−, RD12−	M. bovis
Pasteurized milk soft cheese	Cattle	26	RD screening	RD1+, RD4−, RD9−, RD12−	M. bovis
Pasteurized milk greek style yogurt	Cattle	27	RD screening	RD1+, RD4−, RD9−, RD12−	M. bovis

^a+, positive; −, negative; ITS, 16S-23S rRNA internal transcribed spacer; IS, insertion sequences of M. avium; RD, regions of difference of M. tuberculosis complex; Str., strain.

^bBLAST results displaying highest identity and coverage percentages for sequenced ITS amplicons: identity %, coverage %.

^cDNA extracted from the isolate. Otherwise, the DNA was obtained directly from the product.

^dSequenced ITS amplicon corresponded to the tetraplex real-time PCR (Sevilla et al., 2015).

^eSequenced ITS amplicon corresponding to the PCR described by Richter et al. (1999).