Table 4. Clinical samples analyzed by PCR for M. ulcerans.

	No. of suspected BUD cases	Samples analyzed by PCR
		Laboratory	IS2404 PCR assay	Swaba	FNAb	Punchc	Total
Phase I d	16	DITM	Standard PCR	6	16	13	35
			qPCRe	3/6	6/16	3/13	12/35
		Total f		6	16	13	35
Phase II g	66	INH	DRB PCR	33	44	22	99
		DITM	Standard PCR	33	44	22	99
			qPCRe	6/33	15/44	9/22	30/99
		Total f		66	88	44	198
Total -phase I and II	82			72	104	57	233

Table 4 indicates all samples tested by PCR at IHN and DITM. During the initial phase (phase I) samples were analyzed by standard gel-based IS2404 PCR at DITM. During the second phase (phase II) parallel samples were subjected to IS2404 dry-reagent based (DRB) PCR at INH and standard IS2404 PCR at DITM. During both phases all samples tested negative in standard PCR were subjected to re-testing by IS2404 quantitative real-time PCR (qPCR) at DITM.

^aSwab, DNA extracts prepared from swab samples.

^bFNA, DNA extracts prepared from fine-needle aspirate samples.

^cPunch, DNA extracts prepared from 3 mm punch biopsy samples.

^dPhase I, initial phase of implementation of the national reference laboratory at INH from September through December 2010.

^eOnly samples tested negative in standard IS2404 PCR were subjected to IS2404 qPCR at DITM.

^fTotal amount of samples tested by DRB- and Standard PCR during the corresponding phases.

^gPhase II, transitional phase of implementation of the national reference laboratory at INH from January 2011 through April 2012.