TABLE 3.

Carbapenemase-encoding contigs identified in CNSC genomes

Isolate_contig	Length (bp)	Circulara	Replicon(s)	Carbapenemase gene	Carbapenemase-carrying element	Additional acquired antimicrobial resistance gene(s)b
RS77_21	10,011	No	None	blaKPC-3	Tn4401b-like	None
RS226_4	43,621	Yes	RepA	blaKPC-2	Tn4401-like	blaTEM-1B
RS259_9	21,420	Yes	None	blaNDM-1	Class 1 integron	aac(3)-IId, aac(6′)-Ib-cr, aadA16, arr-3, catB3, dfrA27, mph(A), sul1
YDC608_5	172,511	Yes	IncA/C2	blaKPC-3	Tn4401b-like	aac(6′)-Ib, aadA1, ant(2′')-Ia, blaOXA-9, blaSHV-7, blaTEM-1A
YDC638-3_3	213,257	Yes	IncA/C2	blaKPC-3	Tn4401b-like	aac(6′)-Ib, aac(6′)-Ib-cr, aadA1, ant(2”)-Ia, blaOXA-9, blaSHV-7, blaTEM-1A, qnrA1, sul1
YDC645_3	44,364	Yes	RepA	blaKPC-2	Tn4401-like	None
YDC661_9	15,031	No	None	blaKPC-3	Tn4401b-like	None
YDC667-1_41	4,894	No	None	blaKPC-3	Incomplete Tn4401	None
YDC693_4c	258,721	Yes	IncA/C2, IncN	blaKPC-3	Tn4401-like	aac(6′)-Ib, aadA1, blaOXA-9, blaSHV-7, blaTEM-1A, dfrA14
YDC697-2_6c	62,530	Yes	IncN	blaKPC-3	Tn4401-like	dfrA14
YDC849-1_2	160,983	Yes	IncA/C2	blaNDM-1	Class 1 integron	aac(3)-Iid, aac(6′)-Ib-cr, aadA16, aph(3′')-Ib, aph(3′)-Ia, aph(6)-Id, arr-3, catB3, dfrA27, floR, mph(A), qnrS1, sul1, sul2, tet(A)
YDC876_2d	176,497	Yes	IncA/C2	blaKPC-3	Tn4401b-like	aac(6′)-Ib, aac(6′)-Ib-cr, aadA1, ant(2′')-Ia, blaOXA-9, blaSHV-7, blaTEM-1A, qnrA1, sul1
YDC876_4d	78,220	Yes	IncL/M	blaKPC-3	Tn4401b-like	aac(6′)-Ib, aac(6′)-Ib-cr, aadA1, blaOXA-9, blaTEM-1A
YDC880_4	88,095	Yes	IncL/M	blaKPC-3	Tn4401-like	aadA2, blaSHV-30, dfrA12, sul1

^aCircular contigs were identified through hybrid assembly with Unicycler (25).

^bAntimicrobial resistance genes were identified by querying the ResFinder database (30).

^cContigs from same-patient isolates.

^dContigs from the same isolate.