Table 2.

Antibiotic resistance genes (ARGs) detected in this study using different approaches (reads, contigs and bins) with the NCBI bacterial antimicrobial resistance reference gene database, chromosomal mutations detected using ResFinder, and antibiotic resistance phenotype observed by the conventional antibiotic susceptibility testing (AST).

Sample no.	Conventional antibiotic susceptibility test	Chromosomal mutations	ARGs detected from shotgun-metagenomics
			Reads	Contigs	Bins
1	Penicillin		blaZ, tet38	fosB, blaZ, tet38
2	Penicillin		blaZ, tet38	blaZ, tet38
3		grlA	tet38	tet38
4	Penicillin			fosB, blaZ, tet38
5		grlA	tet38	tet38
6	Penicillin	grlA		tet38	tet38
7	Penicillin		tetM, tet38	fosB, tetM, tet38	fosB, tet38
8			tet38, tetM	tet38
9	Penicillin		tet38, tetM	fosB, tetM, tet38	fosB, tet38
10		grlA		tet38
11				fosB, tet38, blaZ
12	Penicillin Fusidic acid			fosB, blaZ, tet38
13				blaZ, tet38
14	Penicillin		blaZ	fosB, blaZ, tet38
15	Penicillin	grlA	blaZ, tet38	blaZ, tet38
16	Penicillin Fusidic acid		blaZ, tet38	fosB, blaZ, tet38
17				tet38
18	Penicillin Fusidic acid	grlA		blaZ, tet38
19	Penicillin Fusidic acid		blaZ, tet38	fosB, blaZ, tet38
PC			tet38	fosB, tet38