Table 2.

Mutations in TA systems.

Event	TA loci	Loc.	Mut.	Clone type	Patient	Isolate	Est. del.	Infection age	Comment
Insertion in antitoxin	xre/COG5654	CG	2C	DK23	P22M4	177		0 years	Isolate sampled as one-off, toxin likely functional
Insertion in toxin	xre/COG5654	CG		DK21	P22M4	All			40 kb insertion with phage-like genes
Ns snp in toxin	xre/relE (higAB)	CG	C61T	DK01	P28F1	2009		36 years
Deletion of TA pair	xre/relE (higAB)	CG		DK28	P96F4	202	1.6 kb	0 years	Isolate sampled as one-off
Deletion of TA pair	xre/PIN	CG		DK13	P05M4	117	>40 kb	2.4 years
Stop codon in antitoxin	xre/PIN	CG	T291A		Env.	MG7			Toxin likely functional
Stop codon in antitoxin	xre/PIN	CG	T291A	DK49	P72F4	341		0 years	Isolate sampled as one-off, toxin likely functional
Ns snp in antitoxin	xre/GNAT	CG	A439G	DK36	P77F4	400		2.73 years
Partial loss of GI, TA lost	COG5642/COG5654	GI		DK26	P92F3	268, 273–275	105.5 kb	0.35 year
Partial loss of GI, TA remains	PHD/relE (parDE)	GI		DK24	P22M4	183	43 kb	0.17 year
Partial loss of GI, TA remains	abrB/relE & $merR/PIN$	GI		DK36	P77F4	403	53.4 kb	2.73 years
Complete loss of GI	RHH/relE 90/115-140	GI		DK44	P70F4	334	81 kb	1.06 years
Complete loss of GI	RHH/relE 90/115-140	GI		DK02	P06M2	2002	90.6 kb	29 years	Hypermutator
Complete loss of GI	RHH/relE 90/115-140	GI		DK02	P11M2	2006b	90.6 kb	33 years	Hypermutator
Complete loss of GI	RHH/relE 90/115-140	GI		DK02	P40F2	2002	90.6 kb	29 years
Complete loss of GI	RHH/relE 90/115-140	GI		DK02	P43M2	2002	90.6 kb	29 years	Hypermutator
Loss of one out of two GIs	RHH/relE 90/115-140	GI		IT11	P55M4	440	89.1 kb	0.79 year
Partial loss of GI, TA remains	RHH/relE 90/115-140	GI		DK03	P62M4	All but one isolate	40 kb
Partial loss of GI, TA remains	RHH/relE 90/115-140	GI		DK36	P77F4	All but 410, 410.1	50 bp	0.83 year	Integrase deleted
Duplication of GI	xre/COG5654 & merR/PIN	GI		DK26	P92F3	All
Duplication of GI	xre/COG5654 & merR/PIN	GI		DK21	P22M4	181, 182		1.06 years
Partial loss of GI, TA remains	xre/COG5654 & merR/PIN	GI		DK02	P14F1	1973	24 kb	>1 year
Partial loss of GI, TA remains	HEPN/MNT	GI		DK02	P43M2	2002	5 kb	29 years
Partial loss of GI, TA remains	HEPN/MNT	GI		DK02	P33F3	2003.a, 2003.b	>100 kb	30 years	Part of the CG also deleted
Partial loss of GI, TA remains	HEPN/MNT	GI		DK02	P80F1, P11M2	2002.b, 2006.b	18 kb	29 years

List of mutations observed in longitudinally sampled clone types and stop codons observed in clinical and environmental (env.) isolates. The location of a TA pair is given as core genome (CG) or on a genomic island (GI) and the mutation as the nucleotide change within the gene. For deletions, the estimated length in kb is noted, and for each mutation the length of infection of the clone type at sampling time. Stop codons were observed in three antitoxins that were sampled only once for that clone type from two patients and an environmental isolate. The toxins of the antitoxins with stop codons and an insertion were likely still functional, as their sequences were identical to those from other isolates. TA pairs that were identified by TAfinder but not verified by BLASTP analysis are highlighted with green.