Searching for AMRFinder+ annotations

[shaman-narayanasamy]

TLDR: Search the terms "NCBIProtein" and "NCBIFam" in your annotation files for AMRFinder+ results.

Antimicrobial resistance (AMR) is a hot topic globally. Hence, I found myself attempting to quickly screen my genomes or metagenomics assembled genomes (MAGs) for AMR genes. First, the log file will report the total number of AMR genes, like so:

( skipped stdout )
predict & annotate CDSs...
        predicted: 4400 
        discarded spurious: 7
        revised translational exceptions: 3
        detected IPSs: 4184
        found PSCs: 183
        found PSCCs: 16
        lookup annotations...
        conduct expert systems...
                amrfinder: 15
                protein sequences: 681

As you can see, Bakta via AMRFinder+ identified 15 AMR genes from my MAG. To search for these annotations, one would need to search two keywords: "NCBIProtein" and "NCBIFam". The addendum shows the results of my search for those terms, yielding 12 and 3 AMR genes, respectively.

AMRFinder+ comprises two different AMR gene databases, i.e. NCBI proteins and NCBI families. These databases go beyond just AMR genes and cover AMR-related genes, e.g. virulence, secretion, biofilm formation, etc (hence the "+" in AMRFinder+😉).

Feel free to refer to issues #112 and #360 for further reference. Finally, shout out to @oschwengers for the clarification.

Addendum

$ grep "NCBIProtein" 37_MAGScoT_cleanbin_000004.tsv
37_MAGScoT_cleanbin_000004_37_contig_k141_807832	cds	10471	11892	-	GABPFI_00575	espX1	type III secretion system effector EspX1	NCBIProtein:ADD54679.1, RefSeq:WP_000129324.1, SO:0001217, UniParc:UPI000188859E, UniRef:UniRef100_A0A148HVK4, UniRef:UniRef50_A7ZHA9, UniRef:UniRef90_V0ZD67, VFDB:VFC0086, VFDB:VFG034849
37_MAGScoT_cleanbin_000004_37_contig_k141_82060	cds	67603	68835	-	GABPFI_05810	mdtM	multidrug efflux MFS transporter MdtM	COG:COG2814, COG:G, GO:0005886, GO:0015297, GO:0016020, GO:0022857, GO:0046677, GO:0055085, NCBIProtein:AAC77293.1, RefSeq:WP_001137015.1, SO:0001217, UniParc:UPI0001887FC1, UniRef:UniRef100_A0A037YJF6, UniRef:UniRef50_P39386, UniRef:UniRef90_Q8XB84
37_MAGScoT_cleanbin_000004_37_contig_k141_544668	cds	50174	50482	+	GABPFI_07000	asr	acid resistance repetitive basic protein Asr	GO:0042597, NCBIProtein:BAA15331.2, RefSeq:WP_001513309.1, SO:0001217, UniParc:UPI0001888CF0, UniRef:UniRef100_B7NB47, UniRef:UniRef50_Q83RD2, UniRef:UniRef90_Q8X783
37_MAGScoT_cleanbin_000004_37_contig_k141_657477	cds	48727	49860	+	GABPFI_07410	blaEC	BlaEC family class C beta-lactamase	EC:3.5.2.6, NCBIProtein:AAZ85968.1, RefSeq:WP_001376670.1, SO:0001217, UniParc:UPI0001C328F3, UniRef:UniRef100_A0A244BQ89, UniRef:UniRef50_P00811, UniRef:UniRef90_A0A0L6XWZ0
37_MAGScoT_cleanbin_000004_37_contig_k141_657479	cds	66369	69473	+	GABPFI_08560	acrF	multidrug efflux RND transporter permease subunit AcrF	BlastRules:WP_001273238, GO:0005886, GO:0015562, GO:0042910, GO:0098567, GO:0140330, GO:1990281, NCBIProtein:AAC76298.1, RefSeq:WP_001273225.1, SO:0001217, UniParc:UPI0001888F15, UniRef:UniRef100_A0A135PY92, UniRef:UniRef50_P31224, UniRef:UniRef90_P24181
37_MAGScoT_cleanbin_000004_37_contig_k141_700249	cds	62997	63899	-	GABPFI_09745	fieF	CDF family cation-efflux transporter FieF	BlastRules:WP_001076748, BlastRules:WP_003093118, COG:COG0053, COG:P, GO:0005381, GO:0005385, GO:0005886, GO:0006812, GO:0008324, GO:0015086, GO:0015297, GO:0016020, GO:0046872, GO:0055085, NCBIProtein:BAE77395.1, RefSeq:WP_001076742.1, SO:0001217, UniParc:UPI000013B416, UniRef:UniRef100_A7ZUC8, UniRef:UniRef50_Q6CZ45, UniRef:UniRef90_Q8Z2W4
37_MAGScoT_cleanbin_000004_37_contig_k141_129672	cds	24966	25391	-	GABPFI_13120	arsC	glutaredoxin-dependent arsenate reductase	COG:COG1393, COG:P, EC:1.20.4.1, GO:0008794, NCBIProtein:AAA21096.1, RefSeq:WP_000065788.1, SO:0001217, UniParc:UPI00018890C8, UniRef:UniRef100_A0A0Q3BI74, UniRef:UniRef50_P08692, UniRef:UniRef90_B7LSY7
37_MAGScoT_cleanbin_000004_37_contig_k141_704457	cds	225770	230023	-	GABPFI_15330	fdeC	inverse autotransporter adhesin FdeC	BlastRules:WP_000092542, NCBIProtein:ABE05822.1, RefSeq:WP_000092574.1, SO:0001217, UniParc:UPI000188881E, UniRef:UniRef100_A0A234Z2U8, UniRef:UniRef50_A0A7U9H6R6, UniRef:UniRef90_E8Q5F6
37_MAGScoT_cleanbin_000004_37_contig_k141_50438	cds	11717	12901	+	GABPFI_17215	emrD	multidrug efflux MFS transporter EmrD	BlastRules:WP_000828740, BlastRules:WP_000828746, BlastRules:WP_115740452, COG:COG2814, COG:G, GO:0005886, GO:0016020, GO:0022857, GO:0042908, GO:0042910, GO:1990961, KEGG:K08154, NCBIProtein:BAE77620.1, RefSeq:WP_001306726.1, SO:0001217, UniParc:UPI000170F0E3, UniRef:UniRef100_A0A069CII2, UniRef:UniRef50_P31442, UniRef:UniRef90_P31442
37_MAGScoT_cleanbin_000004_37_contig_k141_50438	cds	74884	75456	-	GABPFI_17505	lpfA-O113	long polar fimbria major subunit LpfA-O113	COG:COG3539, COG:N, NCBIProtein:ACB16424.1, RefSeq:WP_000827811.1, SO:0001217, UniParc:UPI00005E2BB7, UniRef:UniRef100_Q2Z2F0, UniRef:UniRef50_Q8VPB9, UniRef:UniRef90_Q8VPB9
37_MAGScoT_cleanbin_000004_37_contig_k141_407343	cds	2650	4347	-	GABPFI_19575	eilA	HilA family transcriptional regulator EilA	BlastRules:WP_001176839, NCBIProtein:CBG36837.1, RefSeq:WP_001176839.1, SO:0001217, UniParc:UPI0001888FC4, UniRef:UniRef100_A0A0P7MTG3, UniRef:UniRef50_A0A236FCE4, UniRef:UniRef90_A0A236FCE4
37_MAGScoT_cleanbin_000004_37_contig_k141_263413	cds	142971	143237	+	GABPFI_23125	ariR	biofilm/acid-resistance regulator AriR	BlastRules:WP_000888772, NCBIProtein:AAC74250.1, RefSeq:WP_000888778.1, SO:0001217, UniParc:UPI0001888C1E, UniRef:UniRef100_A0A023KHX4, UniRef:UniRef90_A0A023KHX4

$ grep "NCBIFam:" 37_MAGScoT_cleanbin_000004.tsv
37_MAGScoT_cleanbin_000004_37_contig_k141_233991	cds	229359	233915	+	GABPFI_04735	sslE	lipoprotein metalloprotease SslE	GO:0005886, NCBIFam:NF037973.1, RefSeq:WP_089627453.1, SO:0001217, UniParc:UPI000B7D23B0, UniRef:UniRef100_UPI000B7D23B0, UniRef:UniRef50_P0CK95, UniRef:UniRef90_P0CK95
37_MAGScoT_cleanbin_000004_37_contig_k141_240457	cds	158459	160636	-	GABPFI_11935	sinH	intimin-like inverse autotransporter SinH	NCBIFam:NF033423.1, RefSeq:WP_033813637.1, SO:0001217, UniParc:UPI0004D7F698, UniRef:UniRef100_UPI0004D7F698, UniRef:UniRef50_G9Y5J8, UniRef:UniRef90_A0A6D0I8R1
37_MAGScoT_cleanbin_000004_37_contig_k141_129672	cds	28505	28867	-	GABPFI_13135	arsD	arsenite efflux transporter metallochaperone ArsD	GO:0003677, GO:0045892, GO:0046685, NCBIFam:NF033727.1, SO:0001217, UniRef:UniRef50_P52148, UniRef:UniRef90_P52148