Extended role for insertion sequence elements in the antibiotic resistance of Bacteroides

Table 1 A list of the related species comprising the ‘Bacteroides fragilis group’ at present

Bacteroides			Parabacteroides
B. acidifaciens	B. fluxus	B. propionifaciens	P. distasonis1,2
B. barnesiae	B. fragilisa,b	B. pyogenes	P. goldsteinii1
B. caccae1,2	B. galacturonicus	B. rodentium	P. gordonii
B. cellulosilyticus	B. gallinarium	B. salanitronis	P. johnsonii
B. chinchillae	B. graminisolvens	B. salyersiae1	P. merdae1,2
B. clarus	B. helcogenes	B. sartorii
B. coagulans	B. heparinolyticus	B. stercoris1,2
B. coprocola	B. intestinalis1	B. thetaiotaomicron1,2
B. coprophilus	B. massiliensis1	B. uniformis1,2
B. coprosuis	B. nordiia	B. vulgatus1,2
B. dorei	B. oleiciplenus	B. xylanisolvens
B. eggerthii1,2	B. ovatus1,2	B. xylanolyticus
B. faecis	B. paurosaccharolyticus	B. zoogleoformans
B. finegoldii	B. plebeius

¹The main pathogenic species of Bacteroides that were included in an antibiotic susceptibility study and are most frequently isolated from clinical specimens; ²The 10 Bacteroides species earlier comprising the B. fragilis group are marked with a superscript b.

Table 2 The 5-nitroimidazole resistance nim genes of interest for Bacteroides

Nim gene type	Carrying genetic element	Activating IS	No. of isolates1
nimA
	pIP417 (7.7 kb)	IS1168	10[102,114,115]
	10 kb uncharacterized plasmid	IS1168	2[102]
	8.2 kb uncharacterized plasmid	IS614	1[102]
	Chromosomal	IS1168 or Unknown	3[102]
	Unknown	IS1168	12[115]
	Unknown	IS1169	1[116]
nimB
	Chromosomal	IS1168 or IS612 or IS614	8[102,114]
	Unknown	IS1168	3[116]
nimC
	pIP419 (10 kb)	IS1170	4[115]
	Chromosomal	IS1170	2[102]
	Unknown	IS1170	2[63,116]
nimD
	pIP421 (7.3 kb)	IS1169	1[102,117]
	Chromosomal	Unknown	1[102]
	Unknown	IS1169	6[116]
nimE
	pBF388c (pWAL610, 8.3 kb)	ISBf6	5[102,118]
nimF
	Chromosomal	Unknown	1[116]
nimG
	Unknown	Unknown	1[63]
nimH
	Unknown	Unknown	-2

¹The number if isolates with the given genotypes are indicated with references;

²Taken from GenBank (http://www.ncbi.nl.nih.gov, acc. no. FJ969397).

Table 3 The insertion sequence elements involved in the up-regulation of antibiotic resistance genes in Bacteroides

IS family1	Group1	IS2	Activated genes
IS4	ISPepr1
		IS943	cfiA
		ISBf8	cfxA
IS5	IS5
		IS1186 (IS1168)	cfxA, cfiA, nimA, nimB
		IS1169	cfiA, nimA, nimD
	IS1031
		ISBf6	nimE
IS21	-
		ISBf1	cepA
IS982	-
		IS1187	cfiA
IS31380	IS942
		IS942	cfiA
		IS1170	nimC
		IS612	cfiA, nimB
		IS613	cfiA
		IS614	cfxA, cfiA, nimB
		IS615	cfiA
	-
		IS1188	cfiA
		IS4351	ermF, cfiA
		IS616	cfiA

¹The IS families and the subgroups within them (taken from IS Finder)[77]; - indicates no further classification;

²The species of IS elements activating the resistance genes of Bacteroides spp.; the mosaics and isoforms are not indicated. IS: Insertion sequence.