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Table 1 Sequences used for synthetic metagenome creation

From: Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools

Sequence Identifier (SRA)a

Strain

Description

ARGsb

Resistance of Interest

ARG Targetc

Reference

51299a

ATCC 51299

Enterococcus faecalis

catA8, aph(3’)-IIIa, ant(6)-Ia, vanW-B, vanY-B, vanS-B, vanR-B, vanH-B, vanX-B, vanB, Isa(A), erm(B), dfrE, sat4

Vancomycin

vanB

[39, 40]

SRR25084145

DT10023001

Escherichia coli

tetB, tetA, sul1, sul2, sul3, qacEdelta1, mcr-1.1, blaTEM-1, aph(6)-Id, aph(3’)-Ia, aph(3’’)-Ib, addA2, blaEC-19, catA1, cmlA1, dfrA1, aadA1 (multiple copies)

Colistin

mcr-1.1

This study

SRR25084104

OLC1107

Klebsiella pneumoniae

blaCTX-M-15, oqxA10, blaSHV-148, fosA (multiple copies), oqxB

ESBL

blaCTX-M-15

This study

SRR10830862

CFIAFB20160069

Listeria monocytogenes

tetM, fosX, bcrABC

Tetracycline

tet(M)

[7]

SRR10859129

CFIAFB20130200

Salmonella enterica ser. Heidelberg

blaCMY-2

ESBL

blaCMY-2

[37]

SRR3053167

 

Beef fecal metagenome

aad9,aadA9,aadE,ant(6)-Ia,ant(6)-Ib,ant(9)-Ia,aph(3')-IIIa,blaACI-1,blaEC-18,cblA,cfr(C),cfxA_gen,cfxA6,cmx,erm(33),erm(A),erm(B),erm(C),erm(G),erm(Q),erm(T),erm(X),lnu(AN2),lnu(C),lnu(G),mef(A),mef(En2),mph(B),msr(D),sat4,spw,str,tcrB,tet(32),tet(33),tet(40),tet(44),tet(B),tet(C),tet(M),tet(O),tet(Q),tet(T),tet(W)

NA

[26]

SRR7414924

 

Lettuce metagenome

aac(2')-Ib,aac(2')-Ic,aac(3)-IV,aac(6')-Ie_fam,aacA-STR-10,aacA34,aadA11,aadA2,aadA6,ant(3'')-IIc,ant(6)-Ia,aph(3')-IIa,aph(4)-Ia,aph(6)-Id,aph(6)-Smalt,BcII,bla1,blaADC-151,blaCME-1,blaIND-9,blaL1,blaOXA-308,blaOXA-571,blaOXA-60,blaOXA-658,blaSPU-1,blaTEM-123,bleO,catA9,cfr-Cb,cipA,cmlR,cmx,erm(A),erm(X),erm(X),estDL136,floR,fosB_gen,fosB-251804940,lsa(B),mecI_of_mecC,mef(A),mgt,mphL,msr(D),oleD,oqxB12,oqxB16,otr(A),rgt1438,rox,rph,rphC,rphD,sul1,sul2,tet(C),tet(G),tet(O),tet(V),tetA(P),vanA-Pa,vanI,vanJ,vanK-Sc,vanM,vanO,vanR-A,vanR-O,vanS-O,vanX-Sc,vga(B)

NA

[41]

  1. Abbreviations: SRA sequence read archive, ARG antimicrobial resistance gene, ESBL extended spectrum-β-lactamase, ATCC American Type Culture Collection
  2. aData for ATCC 51299 strain (Catalog Number: 51299) is not available through the SRA. Raw sequence data locations for ATCC strains can be found on the ATCC-Bioinformatics github [40]
  3. b(multiple copies) is listed next to gene(s) which were detected in multiple locations within the isolates’ genome. Isolate sequences’ AMR results are for genes with ≥ 80% template coverage. Beef and lettuce metagenome ARGs include all hits from analysis of raw-sequence data (1.0% coverage to 100% coverage)
  4. cThe target ARG encoded by corresponding isolate that is focused on in this study
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BMC Microbiology

ISSN: 1471-2180

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