Table 3 Open in new tab Non-redundant...

Gene ID	Length (aa)	Resistance	Number of sequences	Example of pathogen (NCBI taxon ID)	Gene	Transcript
W56_28340_1^a^,^b^,^c	260	Aminoglycoside	ANT3	3	A. baumannii (509173)	12	5	10	8
W54_36555_1^a^,^b^,^c	265	Aminoglycoside	APH(3’)	9	S. epidermidis (176279)	12	3	7	2
W54_1320_4^a^,^c	144	Aminoglycoside	sat-1	8	B. vulgatus (435590)	12	5	2	0
W56_17638_3^a^,^b^,^c	278	Aminoglycoside	strB	7	K. pneumoniae (272620)	12	8	8	6
W54_14042_1^a^,^c	281	Beta-lactam	OXA-58	5	A. baumannii (405416)	11	4	7	1
W56_739_2^a	425	Beta-lactam	ampG	6	B. vulgatus (435590)	12	7	0	0
W70_15043_2^a^,^b^,^c	420	Chloramphenicol	cmlA	5	K. pneumoniae (272620)	12	2	9	5
W60_5396_4^a^,^c	250	Macrolide	ermB	15	E. faecalis (226185)	12	11	12	12
W54_264_15^a	377	Multidrug	mexE	12	B. vulgatus (435590)	12	12	1	0
W71_4945_1^a^,^b^,^c	309	Sulfonamide	sul1	47	S. enterica (423368)	12	12	12	12
W56_1220_2	658	Tetracycline	tetQ	19	B. fragilis (295405)	12	12	9	4
W72_76188_2^a^,^c	104	Trimethoprim	dfrA14	2	B. hermsii (314723)	9	0	2	1

Gene ID

Length (aa)

Resistance

Number of sequences

Example of pathogen (NCBI taxon ID)

Gene

Transcript

Type

Subtype

Influent

Effluent

Influent

Effluent

W56_28340_1^a^,^b^,^c

260

Aminoglycoside

ANT3

A. baumannii (509173)

W54_36555_1^a^,^b^,^c

265

Aminoglycoside

APH(3’)

S. epidermidis (176279)

W54_1320_4^a^,^c

144

Aminoglycoside

sat-1

B. vulgatus (435590)

W56_17638_3^a^,^b^,^c

278

Aminoglycoside

strB

K. pneumoniae (272620)

W54_14042_1^a^,^c

281

Beta-lactam

OXA-58

A. baumannii (405416)

W56_739_2^a

425

Beta-lactam

ampG

B. vulgatus (435590)

W70_15043_2^a^,^b^,^c

420

Chloramphenicol

cmlA

K. pneumoniae (272620)

W60_5396_4^a^,^c

250

Macrolide

ermB

E. faecalis (226185)

W54_264_15^a

377

Multidrug

mexE

B. vulgatus (435590)

W71_4945_1^a^,^b^,^c

309

Sulfonamide

sul1

S. enterica (423368)

W56_1220_2

658

Tetracycline

tetQ

B. fragilis (295405)

W72_76188_2^a^,^c

104

Trimethoprim

dfrA14

B. hermsii (314723)

Gene ID	Length (aa)	Resistance	Number of sequences	Example of pathogen (NCBI taxon ID)	Gene	Transcript
W56_28340_1^a^,^b^,^c	260	Aminoglycoside	ANT3	3	A. baumannii (509173)	12	5	10	8
W54_36555_1^a^,^b^,^c	265	Aminoglycoside	APH(3’)	9	S. epidermidis (176279)	12	3	7	2
W54_1320_4^a^,^c	144	Aminoglycoside	sat-1	8	B. vulgatus (435590)	12	5	2	0
W56_17638_3^a^,^b^,^c	278	Aminoglycoside	strB	7	K. pneumoniae (272620)	12	8	8	6
W54_14042_1^a^,^c	281	Beta-lactam	OXA-58	5	A. baumannii (405416)	11	4	7	1
W56_739_2^a	425	Beta-lactam	ampG	6	B. vulgatus (435590)	12	7	0	0
W70_15043_2^a^,^b^,^c	420	Chloramphenicol	cmlA	5	K. pneumoniae (272620)	12	2	9	5
W60_5396_4^a^,^c	250	Macrolide	ermB	15	E. faecalis (226185)	12	11	12	12
W54_264_15^a	377	Multidrug	mexE	12	B. vulgatus (435590)	12	12	1	0
W71_4945_1^a^,^b^,^c	309	Sulfonamide	sul1	47	S. enterica (423368)	12	12	12	12
W56_1220_2	658	Tetracycline	tetQ	19	B. fragilis (295405)	12	12	9	4
W72_76188_2^a^,^c	104	Trimethoprim	dfrA14	2	B. hermsii (314723)	9	0	2	1

Table 3

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Non-redundant antibiotic resistance genes with 100% identity to known human bacterial pathogens

Gene ID	Length (aa)	Resistance		Number of sequences	Example of pathogen (NCBI taxon ID)	Gene		Transcript
Gene ID	Length (aa)	Type	Subtype	Number of sequences	Example of pathogen (NCBI taxon ID)	Influent	Effluent	Influent	Effluent
W56_28340_1^a^,^b^,^c	260	Aminoglycoside	ANT3	3	A. baumannii (509173)	12	5	10	8
W54_36555_1^a^,^b^,^c	265	Aminoglycoside	APH(3’)	9	S. epidermidis (176279)	12	3	7	2
W54_1320_4^a^,^c	144	Aminoglycoside	sat-1	8	B. vulgatus (435590)	12	5	2	0
W56_17638_3^a^,^b^,^c	278	Aminoglycoside	strB	7	K. pneumoniae (272620)	12	8	8	6
W54_14042_1^a^,^c	281	Beta-lactam	OXA-58	5	A. baumannii (405416)	11	4	7	1
W56_739_2^a	425	Beta-lactam	ampG	6	B. vulgatus (435590)	12	7	0	0
W70_15043_2^a^,^b^,^c	420	Chloramphenicol	cmlA	5	K. pneumoniae (272620)	12	2	9	5
W60_5396_4^a^,^c	250	Macrolide	ermB	15	E. faecalis (226185)	12	11	12	12
W54_264_15^a	377	Multidrug	mexE	12	B. vulgatus (435590)	12	12	1	0
W71_4945_1^a^,^b^,^c	309	Sulfonamide	sul1	47	S. enterica (423368)	12	12	12	12
W56_1220_2	658	Tetracycline	tetQ	19	B. fragilis (295405)	12	12	9	4
W72_76188_2^a^,^c	104	Trimethoprim	dfrA14	2	B. hermsii (314723)	9	0	2	1

Gene ID	Length (aa)	Resistance		Number of sequences	Example of pathogen (NCBI taxon ID)	Gene		Transcript
Gene ID	Length (aa)	Type	Subtype	Number of sequences	Example of pathogen (NCBI taxon ID)	Influent	Effluent	Influent	Effluent
W56_28340_1^a^,^b^,^c	260	Aminoglycoside	ANT3	3	A. baumannii (509173)	12	5	10	8
W54_36555_1^a^,^b^,^c	265	Aminoglycoside	APH(3’)	9	S. epidermidis (176279)	12	3	7	2
W54_1320_4^a^,^c	144	Aminoglycoside	sat-1	8	B. vulgatus (435590)	12	5	2	0
W56_17638_3^a^,^b^,^c	278	Aminoglycoside	strB	7	K. pneumoniae (272620)	12	8	8	6
W54_14042_1^a^,^c	281	Beta-lactam	OXA-58	5	A. baumannii (405416)	11	4	7	1
W56_739_2^a	425	Beta-lactam	ampG	6	B. vulgatus (435590)	12	7	0	0
W70_15043_2^a^,^b^,^c	420	Chloramphenicol	cmlA	5	K. pneumoniae (272620)	12	2	9	5
W60_5396_4^a^,^c	250	Macrolide	ermB	15	E. faecalis (226185)	12	11	12	12
W54_264_15^a	377	Multidrug	mexE	12	B. vulgatus (435590)	12	12	1	0
W71_4945_1^a^,^b^,^c	309	Sulfonamide	sul1	47	S. enterica (423368)	12	12	12	12
W56_1220_2	658	Tetracycline	tetQ	19	B. fragilis (295405)	12	12	9	4
W72_76188_2^a^,^c	104	Trimethoprim	dfrA14	2	B. hermsii (314723)	9	0	2	1

The last four columns show the number of WWTPs in which the resistance gene and its transcripts are detected in the influent or effluent compartment

Found in human bacterial pathogens, but its resistance contigs showing < 95% global nucleotide identity (at least 5% divergence) to the pathogen sequences

Found on both genomes and plasmids of at least one pathogen

Co-located with indicators of mobile genetic elements on the same resistance contig

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