Background
Methods
Search strategy
Selection criteria
-
Reports on AMR in humans from the African region
-
Abstracts and full text available in English
-
Drug sensitivity testing done in a laboratory setting with defined cutoffs for drug susceptibility testing
-
The denominator as total isolates clearly described for population based studies
-
Case reports and case series
-
Reports published before 2013
-
Studies only focused on malaria, HIV or tuberculosis without AMR information
-
Studies without information on total studied isolates
Selection procedure
Data extraction
Article quality assessment
Data analysis
Results
Data and study characteristics
Characteristic | Frequency (%) | References |
---|---|---|
Publication Year | ||
2013 | 67 (46.5) | |
2014 | 39 (27.1) | |
2015 | 35 (24.3) | |
2016 | 3 (2.1%) | |
End of data collection | NA | |
Before 2010 | 17 (11.8) | |
Between 2010 and 2013 | 81 (56.3) | |
After 2013 | 41 (28.5) | |
Not mentioned | 5 (3.5) | |
Study Design | ||
Cross sectional/Case Series | 92 (63.9) | |
Case control | 3 (2.1) | |
Prospective Cohort/Clinical Trial | 11 (7.6) | |
Retrospective | 18 (12.5) | |
Surveillance | 9 (6.3) | |
Not Mentioned | 11 (7.6) | |
Source of Data | ||
In patient | 59 (41.0) | [16, 17, 20, 22, 23, 26, 44‐46, 53, 54, 56, 60‐62, 64, 66, 68, 71, 72, 77, 80, 84, 88, 90‐92, 95, 97, 99, 101, 104, 108, 112, 117‐120, 123, 126‐129, 132, 135, 136, 138, 147, 148, 153, 155, 158, 162, 164, 166, 167, 173] |
Outpatient | 49 (30.0) | |
Both | 12 (8.3) | |
Unknown | 24 (17.4) | |
Type of Infection | ||
Hospital Acquired | 22 (15.3) | |
Community acquired | 58 (40.3) | |
Both | 11 (7.6) | |
Unable to say | 53 (37.5) | |
AMR/Drug susceptibility methodologya
| ||
Disk Diffusion | 118 (81.9) | |
VITEK | 11 (7.6) | |
E-test | 2 (1.4) | |
MIC | 7 (4.9) | |
Not mentioned | 6 (4.2) | |
Laboratory Standard | NA | |
BSAC | 6 4.1) | |
CA-SFM/EUCAST | 15 (10.4) | |
NCCLS/CLSI | 105 (72,9) | |
Not Mentioned | 18 (12.5) | |
Organism identification Methoda
| ||
Morphology | 95 (66.0) | |
API® | 17 (11.8) | |
VITEK | 6 (4.2) | |
NAAT | 3 (2.1) | |
MALDI-ToF | 2 (1.4) | |
Not mentioned | 21 (14.6) | |
Lab Accreditation/Quality assurance activities | ||
ISO | 5 (3.5) | |
EQA | 6 (4.2) | |
Not mentioned | 133 (92.3) | |
Age Group | NA | |
Adults | 42 (29.2) | |
Pediatrics and neonatesb
| 34 (23.6) | |
Both adults and pediatrics | 42 (29.2) | |
Neonates only | 4 (2.8) | |
Unknown | 22 (15.3) |
Microbial resistance patterns
Bacteria | No. Studies | HAI N (%) | BSI N (%) | UTI N (%) | AGE N (%) | WI N (%) | Carriage N (%) |
---|---|---|---|---|---|---|---|
S. aureus
| 79 | 17 (21.5) | 17 (21.5) | NS | NS | 22 (27.8) | 10 (12.7) |
S. pneumoniae
| 24 | NA | 8 (33.3) | 1 (4.2) | NS | NS | 4 (16.7) |
E. coli
| 87 | 15 (17.2) | 17 (19.5) | 17 (19.5) | 7 (8) | NS | 2 (2.3) |
Enterobacter spp. | 36 | 3 (8.3) | 8 (22.2) | 8 (22.2) | 1 (2.8) | NS | NA |
Haemophilus influenza
| 7 | NA | NA | NS | NS | NS | NA |
CoNSa
| 27 | 9 (33.3) | 6 (22.2) | 5 (18.5) | NS | 9 (33.3) | NA |
Citrobacter spp. | 19 | 2 (10.5) | 5 (26.3) | 7 (36.8) | NS | NS | NA |
S. Typhi | 28 | 2 (7.1) | 13 (46.4) | 1 (3.6) | 6 (21.4) | NS | 1 (3.6) |
Pseudomonas aeruginosa
| 60 | 17 (28.3) | 11 (18.3) | 8 (13.3) | NS | 20 (33.3) | 2 (3.3) |
Serratia spp. | 7 | 1 (14.3) | 2 (28.6) | NA | NS | NS | 1 (14.3) |
Klebsiella pneumoniae
| 75 | 15 (20) | 21 (28) | 15 (20) | NS | 16 (21.3) | 2 (2.7) |
Proteus spp. | 46 | 10 (21.7) | 8 (17.4) | 10 (21.7) | NS | NS | 1 (2.2) |
Acinetobacter spp. | 17 | 5 (29.4) | 7 (41.2) | 1 (5.9) | NS | 4 (23.5) | NA |
Neisseria meningitidis
| 1 | NA | NA | NS | NS | NS | NA |
Shigella spp. | 8 | NA | NA | NA | 6 (75) | NS | NA |
Campylobacter spp. | 3 | NA | NA | 1 (33.3) | 3 (100) | NS | NA |
Group A Streptococcus
| 18 | 1 (5.6) | 6 (33.3) | NS | NS | 3 (16.7) | 2 (11.1) |
Group B Streptococcus
| 2 | NA | NA | NS | NS | NA | NA |
Listeria monocytogenes
| 2 | NA | 1 (50) | 1 (50) | NS | NA | NA |
Non-Typhoidal Salmonella spp. | 11 | NA | 9 (81.8) | NS | NA | NS | NA |
Neisseria gonorrhoeae
| 11 | NS | NA | 2 (18.2) | NS | NS | NA |
Moraxella spp. | 2 | NS | NA | NS | NS | NS | NA |
Streptococcus spp. | 3 | NA | NA | 1 (33.3) | NS | 1 (33.3) | 1 (33.3) |
Drugs |
Acinetobacter spp.
(N Isolates)
Median (IQR)
|
Citrobacter spp.
(N Isolates)
Median (IQR)
|
Escherichia coli
(N Isolates)
Median (IQR)
|
Haemophilus influenzae
(N Isolates)
Median (IQR)
|
Klebsiella pneumoniae
(N Isolates)
Median (IQR)
|
Neisseria gonorrhoeae
(N Isolates)
Median (IQR)
| Non-Typhoidal Salmonella spp.
(N Isolates)
Median (IQR)
|
Proteus spp.
(N Isolates)
Median (IQR)
|
Pseudomonas aeruginosa
(N Isolates)
Median (IQR)
|
Salmonella enteric serovar Typhi
(N Isolates)
Median (IQR)
|
Shigella spp.
(N Isolates)
Median (IQR)
|
---|---|---|---|---|---|---|---|---|---|---|---|
Amikacin | (240) 32.7(0–63.6) | (29) 5.8(0–15.4) | (5422) 0.2(0–24.5) | *NC | (1458) 12.6(1.6–37.7) | NC | NC | (251) 16.7(0–67.6) | (476) (6.5–50) | (433) 4.9(0.2–15.5) | NC |
Amoxicillin |
NC
|
(71)
78.5(73.4–95.8)
|
(5500)
88.1(81.4–92.6)
|
NC
|
(524)
100(86.8–100)
|
NC
|
NC
|
(409)
82(48.8–91.4)
|
(230)
84.8(19.2–98.2)
|
(150)
69.2(44.0–77.3)
|
NC
|
Ampicillin |
(188)
100(92.5–100)
|
(59)
100(66.1–100)
|
(2951)
86.7(69.2–96.7)
|
(18)
100(76.6–100)
|
(1259)
100(93.4–100)
|
NC
|
NC
|
(685)
42.3(28.3–84.7)
|
(820)
100(94.5–100)
|
(380)
57.8(21.2–75)
|
(110)
51.1(45.0–61.6)
|
Amoxicillin and Clavulanic Acid |
(56)
94.1(15–100)
|
(53)
34.8(0–100)
|
(6764)
43.5(30.8–61.9)
|
(35)
22.2(0–39.5)
|
(2043)
55.4(35.7–73.2)
|
NC
|
(357)
0(0–53.4)
|
(730)
21.2(0–56.3)
|
(852)
50(3.1–91.9)
|
(558)
6.1(0.6–15.1)
|
NC
|
Azithromycin | NC | NC | NC | NC | NC | (199) 4.2(2.2–33.3) | (1120) 0(0–5.2) | NC | NC | (197) 0(0–0.5) | NC |
Cefotaxime | (205) 90.9(41.7–100) | (58) 29.2(9.1–72.8) | (5173) 26.8(8.3–64.5) | NC | (1199) 50(32.5–76.4) | (96) 0(0–3.4) | (1099) 2.1(0–11.7) | (324) 20.8(0.3–57.6) | (288) 88.5(18.3–100) | (509) 0(0–1.2) | NC |
Ceftazidime | (260) 81.5(36.1–90.8) | (60) 45(9.8–78.6) | (2773) 19.5(10.0–55.8) | NC | (1412) 46.5(12.7–62.9) | NC | NC | (463) 30.9(4.7–39.9) | (1216) 29(25–46.9) | (512) 1.2(0–39.0) | (354) 0(0–22.2) |
Ceftriaxone | (69) 74.2(38.3–100) | (116) 25.3(0–77.2) | (2800) 31.5(6.9–47.7) | (88) 20.4(0–57.1) | (1547) 47.3(25–62.8) | (584) 0 | (807) 9(0.2–41.8) | (755) 17(1.1–35.3) | (915) 30.6(4.5–78.5) | (150) 0(0–19.5) | NC |
Cefuroxime | (31) 75(45.8–100) | NC | (3925) 30(19.7–51.2) | NC | (947) 51.9(35.8–83.2) | NC | NC | (124) 30.7(1.1–59.2) | NC | NC | NC |
Cefoxitin | NC | NC | (535) 8.3(2.9–44.1) | NC | NC | NC | NC | NC | NC | NC | NC |
Cefepime | (79) 50(0–75.2) | NC | (957) 21.8(5.8–42.5) | NC | NC | NC | NC | NC | NC | NC | NC |
Cefalotin | NC | NC | (515) 56.9(23.5–63.5) | NC | (154) 55.7(42.4–76) | NC | NC | NC | NC | (145) 6.8(2.4–35.3) | (201) 3.8(0–8.5) |
Chloramphenicol |
(47)
100(60.4–100)
|
(88)
70.8(18.8–91.7)
|
(2963)
40.9(11.3–58.0)
|
(56)
28.6(10.9–100)
|
(1046)
62.8(48.9–91.5)
|
NC
|
(1982)
60.5(34.9–88)
|
(538)
50(14.3–76.4)
|
(691)
67(33.8–91.7)
|
(348)
43.1(25–60)
|
(65)
11.1(9.1–27.8)
|
Ciprofloxacin |
(47)
29.9(12.1–74.9)
|
(147)
10(0–31.2)
|
(7877)
23.2(7.7–35.6)
|
(28)
14.6(3.1–79.2)
|
(2473)
24.3(7.8–35.4)
|
(658)
37.5(30.7–83.9)
|
(1147)
0.4(0–15.7)
|
(924)
7.2(0–27.4)
|
(1083)
16.1(2–38.4)
|
(562)
0(0–11.7)
|
(386)
0(0–5.4)
|
Trimethoprim/ Sulfamethoxazole |
(133)
80.4(54.5–100)
|
(122)
85.7(64.3–100)
|
(7493)
80.7(69.8–85.6)
|
(54)
83.8(0–100)
|
(2093)
67.8(60.5–93.0)
|
(72)
92.6(25–100)
|
(1981)
60.5(40–88.8)
|
(833)
61.3(39.1–78.7)
|
(912)
92(75.7–100)
|
(1001)
52.8(29.4–72.9)
|
(392)
83.3(39.9–88)
|
Doxycycline | NC | NC | (302) 54.5(12.8–72.3) | NC | (531) 67.8(60.5–93.0) | NC | NC | NC | NC | NC | NC |
Erythromycin | NC | NC | (675) 81.6(29.9–86.5) | NC | (444) 58.9(39.8–82.6) | NC | NC | NC | (501) 77.3(40.8–100) | NC | NC |
Gentamicin | (288) 61.1(25–86) | (143) 37.5(0–48.4) | (8282) 29.8(8.4–45.3) | (35) 59.4(8.9–100) | (2691) 41.7(24.1–66.7) | (88) 28.6(0–55.2) | (1657) 11.9(4.9–37) | (1027) 13.5(0–34) | (1554) 29.4(17.7–44.5) | (801) 2.3(0–21.7) | (365) 5.9(0.2–23.2) |
Imipenem | (230) 2(0–23) | NC | (1613) 0.2(0–5.5) | NC | (1002) 0(0–6.3) | NC | NC | (21) 10.7(0–67.8) | (486) 6(0–51.8) | NC | NC |
Levofloxacin | NC | NC | (751) 19.2(8.7–47.6) | NC | (246) 15.6(8.6–62.7) | NC | NC | (138) 42.7(4.7–91.7) | (77) 25.8(16.5–36.5) | NC | NC |
Meropenem | (24) 40(0–44.4) | NC | (3402) 0(0–5.7) | NC | (711) 3.6(0–11.7) | NC | NC | (154) 1(0–1.6) | (138) 15.8(0–32) | NC | NC |
Nalidixic Acid | NC | (39) 42.9(41.7–62.2) | (2960) 36(12.7–53.8) | NC | (507) 35.2(14.8–53) | NC | (1007) 10.6(4.4–19.6) | (166) 59.3(34–93.8) | (101) 78.4(54.2–90.8) | (537) 5.7(0.6–19.3) | (367) 0.6(0–17.3) |
Nitrofurantoin | (27) 60(0–75) | (52) 40.6(25–52.3) | (5087) 14(4.5–25.1) | NC | (957) 24.0(13–54.7) | NC | NC | (257) 56.3(33.1–84.2) | (151) 76.5(65.9–80) | NC | NC |
Norfloxacin | (39) 34.5(6.3–86) | (89) 41(0–35.6) | (876) 25.6(15.0–46.3) | NC | (518) 31.2(5.6–43.6) | NC | NC | (303) 0(0–3.3) | (578) 17(0–75) | NC | NC |
Ofloxacin | NC | NC | (1294) 30.4(9.8–47.9) | NC | (733) 17(0–23.4) | NC | (1007) 73.2(43.7–90.5) | (322) 29(0–67) | NC | NC | NC |
Oxacillin | NC | NC | (411) 91.5(22.2–98.5) | NC | NC | NC | NC | (128) 46.7(11.9–82.9) | (474) 100(33.3–100) | NC | NC |
Penicillin | NC | NC | (43) 62(52.9–90.6) | NC | NC | (564) 75(52.4–100) | NC | NC | NC | NC | NC |
Piperacillin | (78) 50(41.7–75) | NC | (132) 58.4(35.1–95.0) | NC | NC | NC | NC | NC | NC | NC | NC |
Piperacillin/ Tazobactam | (83) 33.6(12.7–80.1) | NC | (235) 21(11.1–30.6) | NC | NC | NC | NC | NC | (95) 14.6(2.6–45.8) | NC | NC |
Tetracycline | (90) 73(62.2–100) | (72) 83.3(45–100) | (2896) 76.2(72.6–87.9) | (43) 25(11.1–25) | (744) 68(58.7–89.4) | (544) 91.7(63.6–100) | (1532) 37.1(22.4–66.3) | (455) 88.2(56.4–95.8) | (352) 100(81.8–100) | (309) 43(7.5–72.3) | (92) 54.5(22.2–71.1) |
Tobramycin | NC | NC | (677) 32(12.3–43.2) | NC | (207) 55(13.0–67.8) | NC | NC | NC | NC | NC | NC |
Antibiotics | CoNS (N Isolates)
Median (IQR)
| Group A Streptococcus
(N Isolates)
Median (IQR)
|
S. aureus
(N Isolates)
Median (IQR)
|
S. pneumoniae
(N Isolates)
Median (IQR)
|
---|---|---|---|---|
Amikacin | NC | NC | (472) 3 (0–8) | NC |
Amoxicillin |
NC
|
(96)
14.3 (0–100)
|
(1090)
78.6 (62.5–91.7)
|
(229)
22.5 (20–32.5)
|
Ampicillin |
(522)
78.9 (41.3–97)
|
(108)
7.9 (0–41)
|
(2355)
85.7 (78.4–93.8)
|
(436)
20 (6.5–37.8)
|
Amoxicillin and Clavulanic Acid |
(228)
31.8 (5–50.7)
|
NC
|
(2413)
23.5 (11.4–40.2)
|
(331)
17.4 (3.4–70)
|
Cefotaxime | (142) 51.2 (28.7–79.3) | NC | (403) 28.1 (2.7–39.5) | (156) 3.6 (0–12.8) |
Cefoxitin | NC | NC | (1717) 10.4 (4.6–33.8) | NC |
Ceftazidime | NC | NC | (1141) 50 (25.8–54.2) | NC |
Ceftriaxone | (366) 43.9 (9.9–65.6) | (155) 0 (0–16.2) | (2206) 38 (11–47) | (690) 2.2 (0–8.8) |
Cefuroxime | (58) 60 (48–68.6) | NC | (686) 49.2 (32.5–62.6) | (267) 6.6 (0.6–19.8) |
Chloramphenicol |
(445)
51.2 (37.4–77.3)
|
(144)
26 (4.6–62.5)
|
(2413)
24.1 (1.3–54.3)
|
(776)
20.7 (0.9–24.9)
|
Ciprofloxacin |
(568)
42.9 (22.9–54.5)
|
(90)
18.9 (10.7–100)
|
(2678)
21.1 (8.5–33.7)
|
(452)
13.5 (4.1–70.1)
|
Clindamycin | NC | (113) 0 (0–7.5) | (1400) 11.7 (0–47.4) | (185) 6.1 (0–13.2) |
Sulfamethoxazole/Trimethoprim |
(496)
66.7 (59.3–85.3)
|
(163)
33.9 (0–64.7)
|
(3948)
66.1 (42.8–84.3)
|
(976)
90.4 (71.4–98.6)
|
Doxycycline |
NC
|
NC
|
(777)
55.5 (40–79.9)
|
NC
|
Erythromycin |
(476)
48 (38.5–76)
|
(197)
10.4 (3.8–55.2)
|
(3796)
33.9 (13–46.4)
|
(785)
11.5 (2.7–21.5)
|
Gentamicin |
(748)
26.5 (22.2–42.1)
|
(83)
24.3 (0–40.8)
|
(4422)
18.7 (1.5–32.1)
|
(322)
24.5 (15.4–88.5)
|
Imipenem | NC | NC | (126) 8 (1.9–28.9) | NC |
Levofloxacin | NC | NC | (1148) 5.9 (0.4–16.1) | NC |
Nalidixic Acid | NC | NC | (292) 73.2 (67.5–82) | NC |
Nitrofurantoin | (89) 14.7 (0–72.2) | NC | (294) 21.8 (4.5–38.2) | NC |
Norfloxacin | NC | (37) 24.3 (0–0) | (1165) 30 (4.8–33) | NC |
Ofloxacin | NC | NC | (1214) 26.4 (6.4–45.1) | NC |
Oxacillin |
(467)
48 (24.5–67.7)
|
(29)
0 (0–75)
|
(2665)
34.5 (12.6–68.2)
|
(270)
40.7 (0–55.7)
|
Penicillin |
(275)
67.4 (31.6–98)
|
(70)
0 (0–16.2)
|
(1991)
90.4 (80.8–96.4)
|
(1125)
26.7 (8.4–33.6)
|
Tetracycline |
(603)
56.6 (41.4–77.2)
|
(37)
25 (0–63.5)
|
(3297)
44.8 (27.7–58.7)
|
(703)
34.4 (18.8–65.4)
|
Vancomycin | (384) 1.6 (0–34.6) | NC | (2079) 2.8 (0–10.2) | (274) 0 (0–10.2) |