Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now?

Figures & data

Table 1 Death Rates Involving Infection, Associated with and Attributable to AMR, in SSA in 2019

SSA Region	Deaths Involving Infection	Deaths Associated with Resistance	Deaths Attributable to Resistance	Deaths Rate per 100,000 Attributable to Resistance	Ref
Western SSA	1,850,000 (1,510,000–2,270,000)	524,000 (412,000–663,000)	125,000 (95,400–161,000)	27.3 (20.9–35.3)	[8]
Southern SSA	334,000 (276,000–399,000)	62,400 (48,400–79,800)	15,300 (11,300–20,400)	19.4 (14.3–25.9)
Eastern SSA	1,310,000 (1,080,000–1,610,000)	366,000 (290,000–464,000)	88,200 (67,000–116,000)	21.4 (16.3–28.1)
Central SSA	418,000 (335,000–520,000)	113,000 (86,600–144,000)	27,200 (19,600–36,400)	20.7 (14.9–27.7)

Abbreviation: SSA, sub-Saharan Africa.

Table 2 Antibiotic Resistance Rates of Clinical Diarrheagenic E. coli (DEC) in SSA

Country	Isolates	Antibiotic Resistance Rates (%) of Clinical DEC Isolates												Ref
		TET	COT	CHL	CAZ	CTX	CIP	NAL	CRO	AMP	AMC	CN	IMI
Nigeria	165	ND	78.2	ND	22.4	12.1	5.5	ND	ND	ND	40	4.2	ND	[37]
South Africa	120	91	96	94	ND	ND	45	ND	ND	98	ND	ND	36	[44]
South Africa	324	84	82	10	38	45	ND	42	ND	80.9	ND	ND	ND	[41]
Tanzania	687	ND	82	20.5	ND	ND	0	ND	ND	80.9	14.4	ND	ND	[42]
Kenya	136	82.8	61.4	62.1	ND	ND	28.3	11	12.4	83.3	26.2	47.6	ND	[40]
Ghana	21	ND	100	ND	100	100	100	ND	ND	ND	ND	81	0	[43]
Ghana	37	ND	80.5	ND	16.1	19.3	ND	ND	ND	ND	ND	0	0	[47]
Ethiopia	73	ND	67.1	ND	ND	6.9	2.7	27.4	ND	ND	64.4	ND	ND	[50]

Abbreviations: TET, tetracycline; COT, cotrimoxazole; CHL, chloramphenicol; CAZ, ceftazidime; CTX, cefotaxime; CIP, ciprofloxacin; NAL, nalidixic acid; CRO, ceftriaxone; AMP, ampicillin; AMC, amoxycillin/clavulanic acid; CN,gentamicin ; IMI, imipenem; ND, not done.

Table 3 Antibiotic Resistance Rates of Clinical Vibrio cholerae in SSA

Country	Serogroup	Antibiotic Resistance Rates (%) of V. cholerae								Ref
		DO	AZM	CIP	NA	SXT	AMP	CN	TET
Uganda	01 Inaba	ND	ND	<10	>50	˃55	100	0	>50	[61]
Nigeria	01 Ogawa	ND	ND	0	ND	50	ND	ND	75	[62]
Ghana	01 Ogawa	2.5	ND	0	ND	95	90	ND	0	[58]
Kenya	01 Inaba & Ogawa	1.0	ND	0	83.2	ND	89.1	0	97	[63]
Mozambique	01 Ogawa	56	13	0	100	75	100	ND	50	[64]

Abbreviations: DO, doxycycline; AZM, azithromycin; CIP, ciprofloxacin; NA, nalidixic acid; SXT, sulfamethoxazole–trimethoprim; AMP, ampicillin; CN, gentamicin; TET, tetracycline; ND, not done.

Figure 1 Resistance elements inserted into the novel pVC_ESBL plasmid in Kenyan cholera strains.

Figure 2 There are three main regions on the pVC_ESBL: SXT R319 carrying the floR-dhfrA1-strA-StrB-sul2 genes, class 1 integron carrying aadB-arr2-bla_TEM1B-cmlA-bla_OXA-10-arr-2-aadA1 cassettes and with sul1 and a truncated qacEΔ1 gene at the 3’ conserved end, and resistance genes inserted into the plasmid backbone encoding resistance to bla_CTX-M-15), aac(3)-IIc that confer resistance to streptomycin, kanamycin, and tobramycin, and a putative gene for tunicamycin resistance.

Table 4 Antibiotic Resistance Rates of Clinical Salmonella enterica Serotype Typhi Isolates in SSA

Country	Antibiotic Resistance Rates (%) of Clinical S. Typhi Isolates										Ref
	Isolates	TET	COT	CHL	CAZ	CTX	CIP	NAL	CRO	AMP
Kenya	144	73	70	72	ND	6	6	7	4	72	[69]
Uganda	18	83	ND	83	ND	ND	0	5.6	0	83	[81]
Ethiopia	6	83.3	50	83.3	0	0	16.7	50	16.7	ND	[82]
Ethiopia	6	ND	66.7	16.7	ND	100	16.7	100	0	83.3	[83]
DRC	470	ND	ND	54.9	ND	ND	24.5	ND	ND	70	[84]
Nigeria	440	100	100	100	ND	27.3	27.3	ND	ND	100	[85]
Zimbabwe	41	>45	ND	>90	ND	ND	22	<5	0	>90	[86]

Abbreviations: TET, tetracycline; COT, cotrimoxazole; CHL, chloramphenicol; CAZ, ceftazidime; CTX, cefotaxime; CIP, ciprofloxacin; NAL, nalidixic acid; CRO, ceftriaxone; AMP, ampicillin; ND, not done.

Table 5 Antimicrobial Resistance Rates of Clinical Salmonella enterica Serotype Typhimurium Isolates in SSA

Country	Antimicrobial Resistance Rates (%) of Clinical S. Typhimurium Isolates											Ref
	Isolates	TET	COT	CHL	CAZ	CTX	CIP	NAL	CRO	AMP	AZM
Gambia	19	10–20	20–30	10–20	ND	ND	0	ND	0	20–30	ND	[112]
Congo	345	ND	95.1	87.6	ND	ND	13.3	ND	3.8	92.5	36.2	[101]
Mali	178	ND	92.1	91.0	ND	ND	ND	ND	0	93.8	ND	[113]
Mozambique	460	16.4	63.9	43.3	ND	ND	0	16.7	0	71.4	ND	[114]
Malawi	294	ND	ND	ND	ND	ND	0.2	ND	0.3	ND	ND	[115]
Kenya	45	20	100	80	ND	0	<5	20	ND	100	ND	[116]

Abbreviations: TET, tetracycline; COT, cotrimoxazole; CHL, chloramphenicol; CAZ, ceftazidime; CTX, cefotaxime; CIP, ciprofloxacin; NAL, nalidixic acid; CRO, ceftriaxone; AMP, ampicillin; AZM, azithromycin; ND, not done.

Table 6 Antimicrobial Resistance Rates of Clinical Salmonella enterica Serotype Enteritidis Isolates in SSA

Country	Antimicrobial Resistance Rates (%) of Clinical S. Enteritidis Isolates											Ref
	Isolates	TET	COT	CHL	CAZ	CTX	CIP	NAL	CRO	AMP	AZM
Gambia	49	80	70–80	80–90	ND	ND	0	0	100	80–90	ND	[112]
Congo	316	ND	84.2	84.2	ND	ND	2.2	ND	0	86.1	0	[101]
Mali	55	ND	56.4	40	ND	ND	ND	ND	18.2	92.7	ND	[113]
Mozambique	133	64.3	66.7	69.1	ND	ND	0	25.2	0	69.1	ND	[114]
Malawi	73	ND	ND	ND	ND	ND	0.5	ND	0.2	ND	ND	[115]

Abbreviations: TET, tetracycline; COT, cotrimoxazole; CHL, chloramphenicol; CAZ, ceftazidime; CTX, cefotaxime; CIP, ciprofloxacin; NAL, nalidixic acid; CRO, ceftriaxone; AMP, ampicillin; AZM, azithromycin; ND, not done.

Table 7 Antimicrobial Resistance Rates of Clinical Acinetobacter baumannii in SSA

		Antimicrobial Resistance Rates (%) of A. baumannii
		MEM	IPM	LVX	CAZ	FEP	CIP	CN	SXT	Ref
Ghana	24	8.3	8.3	25	20.8	16.7	50	50	66.7	[145]
Ghana	87	59.8	ND	67.8	75.9	ND	64.4	72.4	70.1	[149]
Nigeria	34	91.2	82.4	97.1	94	97.1	97.1	97.1	100	[146]
South Africa	141	87	89	ND	90	81	67	74	69	[153]
Ethiopia	102	60.7	ND	ND	100	93.3	74.4	ND	68.2	[154]
Uganda	19	100	100	ND	90	63	63	79	ND	[155]
Kenya	27	88.9	ND	66.7	ND	100	ND	ND	ND	[147]

Abbreviations: MEM, meropenem; IPM, imipenem; LVX, levofloxacin; CAZ, ceftazidime; FEP, cefepime; CIP, ciprofloxacin; CN, gentamicin; SXT, trimethoprim/sulfamethoxazole (co-trimoxazole); ND, not done.

Table 8 Antimicrobial Resistance Rates of Staphylococcus aureus in SSA

Country	Isolates	Antimicrobial Resistance Rates (%) of S. aureus										Ref
		MRSA	DA	VA	PEN	SXT	TET	CIP	ERY	CHL	CN
Kenya	944	27.8	0	4.9	91.9	56.9	33.2	ND	ND	ND	ND	[157]
Uganda	41	38	0	ND	ND	43	56	24	32	24	17	[158]
Ghana	308	3	5	ND	97	4	42	ND	6	ND	3	[159]
Nigeria	217	2.4	ND	ND	97.2	84.3	13.8	ND	ND	ND	N	[160]
South Africa	2709	46	<30	0	ND	<50	<40	<30	<40	ND	<50	[161]
Ethiopia	80	1.25	28.8	0	88.8	5	52.5	1.25	18.8	5	15	[162]
Mozambique	84	8	ND	ND	89	36	59	ND	ND	ND	ND	[163]
Malawi	783	NA	ND	ND	ND	24	ND	19	53	34	23	[172]

Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus; DA, clindamycin; VA, vancomycin; PEN, penicillin; SXT, trimethoprim/sulfamethoxazole (co-trimoxazole); TET, tetracycline; CIP, ciprofloxacin; ERY, erythromycin; CHL, chloramphenicol; CN, gentamicin; ND, not done; NA, not available.

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