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Table 5 A summary of resistant genes detected in humans, animals and environment

From: Antimicrobial use and resistance in food-producing animals and the environment: an African perspective

MethodologyAMR genesReference
HumanAnimalsEnvironment 
Disc diffusion, CHROMagar™, Etest, MALDI-TOF-MS, MLST, PFGE, PCR, SequencingblaCTX-M-15, blaTEM-1, blaOXA-1,
aac(6′)- Ib-cr
blaCTX-M-15,
blaOXA-1,
aac(6′)- Ib-cr, blaTEM-1
blaCTX-M-15,
blaTEM-1, blaOXA-1,
aac(6′)- Ib-cr
[64]
Disk diffusion, PCR, sequencingblaTEM-1, blaOXA-10,
blaCTX-M-15
blaTEM-1,
blaTEM-57
 [65]
PRISMA guidelinesblaCTX-M-15blaCTX-M-15blaCTX-M-15[66]
MacConkey agar, Disk diffusion, PCRblaKPC, blaOXA-48, blaNDMblaKPC, blaOXA-48, blaNDMblaKPC, blaOXA-48, blaNDM[67]
PRISMA guidelinesblaSHV, blaTEM,
blaZ, tet(A), tet(B),
tet(C), tet(K), vanA,
vanB, vanC1, ermB,
vanC2/3,erm, aac (6′)-aph (2″), aac(6′)-lb-cr, blaGES, blaGIM, blaIMP, blaKPC, blaNDM,
blaNDM-1, blaPER, blaSIM, blaSPM, blaVIM, cfiA,
cfxA, CjgyrA, CmeB, eis, embB, frxA, gidB, gyrA, gyrB, inhA, katG, mcr-1
plasmid, mtrR, mupA, nimA-J, parC, parE, penA, pilQ, pncA, ponA
porB1b (penB), qepA, qnrA, qnrB, qnrC, qnrD,
qnrS, rdxA, rpoB, Tet(O), tet(Q)
blaSHV, blaTEM,
blaZ, tet(A), tet(B), tet(C), tet(K), vanA,
vanB, vanC1, ermB,vanC2/3, erm, ant (3″)-la, ermA, mphC, msrA
blaSHV, blaTEM,
blaZ, tet(A), tet(B), tet(C), tet(K), vanA, vanB, vanC1, ermB,
vanC2/3, erm, aadA, aadA1, Bla, cat I, cat II, cmlA1,
dfr18, dfrA1, dfrA1, floR, mefA, srC,
strB, sul3,
tet(D), tet(E), tet(G), tet(H),
tet(J), tet(L), tet(Y)
[68]
MacConkey with 2 mg/L cefotaxime,
Disc diffusion,
VITEK®2 system
and WGS
 blaCTX-M-15, blaTEM-1, blaOXA-1, aac(6′)- Ib-cr, strA, strB, aac(3)-IId, aadA1, qnrB1, qnrS1, sul1, sul2, dfrA14, dfrA17,dfrA1,dfrA18, tet(A),
dfrA30, dfrA5, dfrA7, tet(D), blaSHV-11, blaSHV-1, blaACT-15, blaMIR-3, blaCMY-37, blaCMY-49, aadA2, aac(3)-IIa, qnrB29, qnrB48, oqxA, oqxB.
blaCTX-M-15, blaTEM-1, blaOXA-1, aac(6′)- Ib-cr, strA, strB, aac(3)-IId, aadA1, qnrB1, qnrS1, sul1, sul2, dfrA14, dfrA17, dfrA1, dfrA18,
dfrA30, dfrA5, dfrA7, tet(A), tet(D),
aadA5
[69]
MacConkey agar with 2 mg/mL cefotaxime, ChromAgar, Disk diffusion, WGS VITEK®2 blaCTX-M-15, strA, strB, aac(6)-Ib-cr, qnrS1 [70]
MacConkey agar with 2 mg/mL cefotaxime, Disk diffusion, VITEK®2, WGS CHROMagar,blaCTX-M-15, aac(6′)Ib-cr, strA, strB, qnrS1  [71]
MacConkey broth, Disc diffusion, API 20E, PCR, SequencingTet(B)Tet(B) [41]
Disk diffusion, MLST, WGSstrA, strB, aadA1, tet(B), blaTEM-1B, catA1, sul1, sul2, dfrA1strA, strB, aadA1, tet(B), blaTEM-1B, catA1, sul1, sul2, dfrA1 [72]
API 20E System, MALDI-TOF, PCRblaCTX-M-1, blaCTX-M-15, blaTEMblaCTX-M-1, blaTEM [73]
MacConkey and XLD agar, TSI, API 20 E, Disk diffusion, PCR sul1 and tet(A)sul1 and tet(A)[74]
MacConkey with cefotaxime (2 mg/l), MCA with ciprofloxacin, double-disc synergy test, PCR, MALDI, MLST, PFGEblaTEM-1, blaCTX-M-15, sul1, sul2, tet(B), catA1, oqxA, dfrA17-aadA5, qepA, strA, tet(A), dfr12-orf-aadA2, qnrS1, aadA1, strA-B, tet(D), oqxB, sul3, dfrA7, aadA5, dfr1-sat-aadA1, qnrB1, aac(60)Ib-cr, blaOXA-1, blaSHV-2a, blaCTX-M variant 2blaTEM-1, blaCTX-M-15, sul1, sul2, tet(B), catA1, oqxA, dfrA17-aadA5, qepA, strA, tet(A), dfr12-orf-aadA2, qnrS1, aadA1, qnrB33, qnrB17, qnrB28, blaSHV-62 [75]
Slide agglutination, ETest, PCRblaTEM, blaSHV,
blaCTX-M, tet(A), floR, sul2, dfrA1, dfr18, strA, strB,
qnrVC3, gyrA, gyrB
 blaTEM, blaSHV,
blaCTX-M, tet(A), floR, sul2, dfrA1, dfr18, strA, strB,
qnrVC3, gyrA, gyrB
[76]