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

Kimera, Zuhura I.; Mshana, Stephen E.; Rweyemamu, Mark M.; Mboera, Leonard E. G.; Matee, Mecky I. N.

doi:10.1186/s13756-020-0697-x

Antimicrobial Resistance & Infection Control

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

Methodology	AMR genes			Reference
Methodology	Human	Animals	Environment
Disc diffusion, CHROMagar™, Etest, MALDI-TOF-MS, MLST, PFGE, PCR, Sequencing	bla_CTX-M-15, bla_TEM-1, bla_OXA-1, aac(6′)- Ib-cr	bla_CTX-M-15, bla_OXA-1, aac(6′)- Ib-cr, bla_TEM-1	bla_CTX-M-15, bla_TEM-1, bla_OXA-1, aac(6′)- Ib-cr	[64]
Disk diffusion, PCR, sequencing	bla_TEM-1, bla_OXA-10, bla_CTX-M-15	bla_TEM-1, bla_TEM-57		[65]
PRISMA guidelines	bla_CTX-M-15	bla_CTX-M-15	bla_CTX-M-15	[66]
MacConkey agar, Disk diffusion, PCR	bla_KPC, bla_OXA-48, bla_NDM	bla_KPC, bla_OXA-48, bla_NDM	bla_KPC, bla_OXA-48, bla_NDM	[67]
PRISMA guidelines	bla_SHV, bla_TEM, bla_Z, tet(A), tet(B), tet(C), tet(K), vanA, vanB, vanC1, ermB, vanC2/3,erm, aac (6′)-aph (2″), aac(6′)-lb-cr, bla_GES, bla_GIM, bla_IMP, bla_KPC, bla_NDM, bla_NDM-1, bla_PER, bla_SIM, bla_SPM, bla_VIM, 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)	bla_SHV, bla_TEM, bla_Z, tet(A), tet(B), tet(C), tet(K), vanA, vanB, vanC1, ermB,vanC2/3, erm, ant (3″)-la, ermA, mphC, msrA	bla_SHV, bla_TEM, bla_Z, 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		bla_CTX-M-15, bla_TEM-1, bla_OXA-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), bla_SHV-11, bla_SHV-1, bla_ACT-15, bla_MIR-3, bla_CMY-37, bla_CMY-49, aadA2, aac(3)-IIa, qnrB29, qnrB48, oqxA, oqxB.	bla_CTX-M-15, bla_TEM-1, bla_OXA-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		bla_CTX-M-15, strA, strB, aac(6)-Ib-cr, qnrS1		[70]
MacConkey agar with 2 mg/mL cefotaxime, Disk diffusion, VITEK®2, WGS CHROMagar,	bla_CTX-M-15, aac(6′)Ib-cr, strA, strB, qnrS1			[71]
MacConkey broth, Disc diffusion, API 20E, PCR, Sequencing	Tet(B)	Tet(B)		[41]
Disk diffusion, MLST, WGS	strA, strB, aadA1, tet(B), bla_TEM-1B, catA1, sul1, sul2, dfrA1	strA, strB, aadA1, tet(B), bla_TEM-1B, catA1, sul1, sul2, dfrA1		[72]
API 20E System, MALDI-TOF, PCR	bla_CTX-M-1, bla_CTX-M-15, bla_TEM	bla_CTX-M-1, bla_TEM		[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, PFGE	bla_TEM-1, bla_CTX-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, bla_OXA-1, bla_SHV-2a, bla_{CTX-M variant 2}	bla_TEM-1, bla_CTX-M-15, sul1, sul2, tet(B), catA1, oqxA, dfrA17-aadA5, qepA, strA, tet(A), dfr12-orf-aadA2, qnrS1, aadA1, qnrB33, qnrB17, qnrB28, bla_SHV-62		[75]
Slide agglutination, ETest, PCR	bla_TEM, bla_SHV, bla_CTX-M, tet(A), floR, sul2, dfrA1, dfr18, strA, strB, qnrVC3, gyrA, gyrB		bla_TEM, bla_SHV, bla_CTX-M, tet(A), floR, sul2, dfrA1, dfr18, strA, strB, qnrVC3, gyrA, gyrB	[76]

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