Introduction
Materials and methods
Study design, setting and population
Participant recruitment
Specimen collection and processing
Nucleic acid extraction
Molecular identification of the S. aureus isolates
Molecular characterisation
Statistical analysis
Results
S. aureus colonisation in cases and controls
Explanatory variable | Umtata | Cape Town | ||||||
---|---|---|---|---|---|---|---|---|
Total, n (%) | Case, n (%) | Control, n (%) | p-value | Total, n (%) | Case, n (%) | Control, n (%) | p-value | |
Total | 111 (100) | 58 (52) | 53 (48) | 0.502a | 74 (100) | 43 (58) | 31 (42) | 0.049a |
Age (months) | ||||||||
Mean [standard deviation] | 21.27 [7.15] | 21.03 [7.41] | 21.53 [6.90] | 0.718 | 24.19 [7.37] | 23.98 [7.44] | 24.48 [7.38] | 0.773 |
Sex | ||||||||
Female | 42 (39) | 24 (43) | 18 (34) | 0.431 | 36 (49) | 19 (44) | 17 (55) | 0.480 |
Male | 67 (61) | 32 (57) | 35 (66) | 38 (51) | 24 (56) | 14 (45) | ||
AD severity | ||||||||
Moderate | 23 (40) | 23 (40) | – | 21 (49) | 21 (49) | – | ||
Severe | 35 (60) | 35 (60) | – | 22 (51) | 22 (51) | – | ||
Atopic disease | ||||||||
Food allergy | 11 (10) | 10 (17) | 1 (2) | 0.009 | 9 (12) | 9 (21) | 0 (0) | 0.008 |
Asthma | 0 (0) | 0 (0) | 0 (0) | 1 (1) | 1 (3) | 0 (0) | 1.000 | |
Allergic rhinitis | 7 (8) | 1 (2) | 6 (11) | 0.242 | 1 (1) | 1 (3) | 0 (0) | 1.000 |
Mode of birth | ||||||||
Caesarean section | 25 (23) | 14 (24) | 11 (21) | 0.821 | 33 (46) | 20 (49) | 13 (42) | 0.637 |
Vaginal | 86 (77) | 44 (76) | 42 (79) | 39 (54) | 21 (51) | 18 (58) | ||
Breastfeeding | 35 (32) | 10 (17) | 25 (47) | 0.001 | 9 (12) | 7 (16) | 2 (6) | 0.288 |
Antibiotic exposure | 92 (82) | 49 (83) | 43 (81) | 0.810 | 54 (72) | 30 (70) | 24 (77) | 0.598 |
Immunisation status | ||||||||
Complete | 107 (96) | 56 (95) | 52 (98) | 0.620 | 64 (86) | 33 (77) | 31 (100) | 0.004 |
Incomplete | 4 (4) | 3 (5) | 1 (2) | 10 (14) | 10 (23) | 0 (0) | ||
Large family a | 62 (55) | 30 (52) | 32 (60) | 0.445 | 24 (32) | 14 (33) | 10 (32) | 1.000 |
Animal exposure | 93 (84) | 39 (67) | 53 (100) | 0.001 | 2 (3) | 2 (6) | 0 (0) | 0.495 |
Parental education | ||||||||
Primary | 8 (7) | 2 (3) | 6 (11) | 0.001 | 1 (1) | 1 (2) | 0 (0) | 0.025 |
Secondary | 70 (63) | 31 (53) | 39 (74) | 33 (45) | 14 (33) | 19 (61) | ||
Tertiary | 31 (28) | 25 (43) | 6 (11) | 40 (54) | 28 (65) | 12 (39) | ||
Other | 2 (2) | 0 (0) | 2 (4) | 0 (0) | 0 (0) | 0 (0) | ||
Maternal factors | ||||||||
Animal exposure | 96 (86) | 44 (76) | 52 (98) | 0.001 | 4 (60) | 4 (11) | 0 (0) | 0.120 |
Pregnant smoking | 1 (1) | 0 (0) | 1 (2) | 0.482 | 3 (45) | 0 (0) | 3 (10) | 0.094 |
Smoking | 1 (1) | 0 (0) | 1 (2) | 0.477 | 4 (6) | 1 (3) | 3 (10) | 0.324 |
Asthma | 2 (2) | 2 (3) | 0 (0) | 0.496 | 6 (8) | 4 (10) | 2 (6) | 1.000 |
Allergic rhinitis | 4 (4) | 4 (7) | 0 (0) | 0.120 | 5 (68) | 4 (10) | 1 (3) | 0.387 |
Atopic dermatitis | 2 (2) | 2 (3) | 0 (0) | 0.496 | 3 (4) | 2 (5) | 1 (3) | 1.000 |
Food allergy | 3 (3) | 2 (3) | 1 (2) | 1.000 | 1 (1) | 1 (2) | 0 (0) | 1.000 |
Paternal factors | ||||||||
Smoking | 15 (14) | 9 (16) | 6 (12) | 0.589 | 20 (31) | 11 (31) | 9 (31) | 1.000 |
Asthma | 3 (3) | 3 (5) | 0 (0) | 0.245 | 0 (0) | 0 (0) | 0 (0) | |
Allergic rhinitis | 3 (3) | 3 (5) | 0 (0) | 0.245 | 7 (10) | 7 (17) | 0 (0) | 0.018 |
Atopic dermatitis | 1 (1) | 1 (2) | 0 (0) | 1.000 | 2 (3) | 2 (5) | 0 (0) | 0.505 |
Food allergy | 1 (1) | 1 (2) | 0 (0) | 1.000 | 1 (1) | 1 (2) | 0 (0) | 1.000 |
Household factors | ||||||||
Electricity + gas | 69 (62) | 56 (97) | 13 (25) | 0.001 | 66 (99) | 35 (97) | 31 (100) | 1.000 |
Kerosene + paraffin | 64 (58) | 44 (76) | 20 (38) | 0.001 | 43 (64) | 21 (58) | 22 (71) | 0.317 |
Paraffin | 38 (34) | 6 (10) | 32 (60) | 0.001 | 0 (0) | 0 (0) | 0 (0) | |
Indoor fire | 4 (4) | 2 (3) | 2 (4) | 1.000 | 0 (0) | 0 (0) | 0 (0) | |
Outdoor fire | 49 (44) | 12 (21) | 37 (70) | 0.001 | 0 (0) | 0 (0) | 0 (0) | |
Wood + fire | 31 (28) | 4 (7) | 27 (51) | 0.001 | 0 (0) | 0 (0) | 0 (0) |
Risk factors associated with S. aureus colonisation across the locations
Explanatory variable | Colonised a, n (%) | Not colonised, n (%) | OR [95% CI] | p-value | aOR [95% CI] | p-value |
---|---|---|---|---|---|---|
AD: case | 31 (28) | 27 (24) | 7.54 [2.92–19.47] | 0.000 | 8.02 [1.28–50.37] | 0.026 |
Sex: male | 21 (19) | 46 (42) | 0.74 [0.33–1.67] | 0.469 | 0.83 [0.32–2.16] | 0.696 |
Child characteristics | ||||||
Breastfeeding | 10 (9) | 25 (23) | 0.69 [0.29–1.63] | 0.395 | 1.46 [0.48–4.47] | 0.503 |
Allergic rhinitis | 1 (1) | 6 (7) | 0.43 [0.05–3.79] | 0.449 | Excluded | |
Asthma § | 0 (0) | 0 (0) | Omitted d | Excluded | ||
Food allergy | 5 (5) | 6 (5) | 1.69 [0.48–5.95] | 0.413 | Excluded | |
Mode of delivery: vaginal | 29 (26) | 57 (51) | 0.9 [0.36–2.29] | 0.833 | Excluded | |
Incomplete immunisation status | 2 (2) | 2 (2) | 1.97 [0.27–14.58] | 0.506 | Excluded | |
Antibiotic exposure | 33 (30) | 58 (52) | 1.71 [0.57–5.12] | 0.34 | 1.54 [0.39–6] | 0.536 |
Large family size b | 15 (14) | 35 (32) | 0.71 [0.32–1.57] | 0.395 | 0.94 [0.36–2.44] | 0.903 |
Animal exposure c | 27 (24) | 65 (59) | 0.3 [0.11–0.83] | 0.021 | 0.53 [0.11–2.54] | 0.429 |
Fossil fuel exposure | ||||||
Electricity + gas | 31 (28) | 38 (34) | 4.08 [1.59–10.44] | 0.003 | 0.35 [0.05–2.47] | 0.295 |
Kerosene + paraffin | 28 (25) | 36 (32) | 2.88 [1.22–6.77] | 0.015 | 0.69 [0.19–2.49] | 0.571 |
Indoor fire | 1 (1) | 3 (3) | 0.63 [0.06–6.27] | 0.694 | Excluded | |
Outdoor fire | 10 (9) | 39 (35) | 0.31 [0.13–0.73] | 0.008 | 0.54 [0.17–1.67] | 0.283 |
Wood + coal | 3 (3) | 28 (25) | 0.14 [0.04–0.49] | 0.002 | 0.14 [0.02–0.99] | 0.048 |
Maternal factors | ||||||
Allergic rhinitis | 0 (0) | 4 (4) | Omitted d | Excluded | ||
Asthma | 1 (1) | 1 (1) | 1.95 [0.12–32] | 0.641 | Excluded | |
Atopic dermatitis | 1 (1) | 1 (1) | 1.95 [0.12–32] | 0.641 | Excluded | |
Food allergy | 1 (1) | 2 (2) | 0.96 [0.08–10.93] | 0.973 | Excluded | |
Smoking | 0 (0) | 1 (1) | Omitted | Excluded | ||
Pregnant smoker | 0 (0) | 1 (1) | Omitted | Excluded | ||
Animal exposure c | 31 (28) | 65 (59) | 0.55 [0.18–1.64] | 0.28 | 1.93 [0.37–10.16] | 0.438 |
Paternal factors | ||||||
Allergic rhinitis § | 0 (0) | 3 (3) | Omitted | Excluded | ||
Asthma § | 1 (1) | 2 (2) | 0.96 [0.08–10.93] | 0.973 | Excluded | |
Atopic dermatitis § | 0 (0) | 1 (1) | Omitted | Excluded | ||
Food allergy § | 0 (0) | 1 (1) | Omitted | Excluded | ||
Smoking | 5 (5) | 10 (9) | 0.94 [0.3–2.98] | 0.267 | Excluded |
Explanatory variable | Colonised a, n (%) | Not colonised, n (%) | OR [95% CI] | p-value |
---|---|---|---|---|
AD: case | 30 (41) | 13 (18) | 4.2 [1.57–11.2] | 0.004 |
Sex: male | 19 (26) | 19 (25) | 0.74 [0.33–1.67] | 0.469 |
Child characteristics | ||||
Breastfeeding | 6 (8) | 3 (4) | 1.71 [0.39–7.45] | 0.472 |
Atopic dermatitis | ||||
Allergic rhinitis | 1 (1) | 0 (0) | Omitted d | |
Asthma § | 1 (1) | 0 (0) | Omitted d | |
Food allergy | 6 (8) | 3 (4) | 1.71 [0.39–7.45] | 0.472 |
Mode of delivery: vaginal | 22 (31) | 17 (24) | 0.95 [0.37–2.43] | 0.921 |
Incomplete immunisation status | 8 (11) | 2 (3) | 3.76 [0.74–19.09] | 0.11 |
Antibiotic exposure | 31 (42) | 23 (31) | 1.35 [0.48–3.77] | 0.57 |
Large family size b | 9 (12) | 8 (11) | 0.88 [0.3–2.61] | 0.816 |
Animal exposure c | 1 (1) | 1 (1) | 0.86 [0.05–14.3] | 0.915 |
Fossil fuel exposure | ||||
Electricity + gas | 36 (54) | 30 (45) | Omitted d | |
Kerosene + paraffin | 20 (30) | 23 (34) | 0.43 [0.15–1.23] | 0.116 |
Indoor fire | 0 (0) | 0 (0) | Omitted d | |
Outdoor fire | 0 (0) | 0 (0) | Omitted d | |
Wood + coal | 0 (0) | 0 (0) | Omitted d | |
Maternal factors | ||||
Allergic rhinitis | 0 (0) | 5 (7) | Omitted d | |
Asthma | 3 (4) | 3 (4) | 0.76 [0.14–4.06] | 0.751 |
Atopic dermatitis | 1 (1) | 2 (3) | 0.38 [0.03–4.33] | 0.432 |
Food allergy | 1/73 | 0 (0) | Omitted d | |
Smoking | 3 (4) | 1 (1) | 2.65 [0.26–26.82] | 0.41 |
Pregnant smoker | 2 (3) | 1 (1) | 1.76 [0.15–20.45] | 0.65 |
Animal exposure c | 3 (5) | 1 (2) | 2.64 [0.26–26.76] | 0.412 |
Paternal factors | ||||
Allergic rhinitis § | 5 (7) | 2 (3) | 2.08 [0.38–11.52] | 0.4 |
Asthma § | 0 (0) | 0 (0) | Omitted d | |
Atopic dermatitis § | 2 (3) | 0 (0) | Omitted d | |
Food allergy § | 1 (1) | 0 (0) | Omitted d | |
Smoking | 13 (20) | 7 (11) | 1.86 [0.62–5.54] | 0.267 |
Clonal lineages of recovered S. aureus isolates
Distribution of S. aureus spa clonal lineages across locations by AD disease and severity
spa-CC | Umtata | Cape Town | ||||
---|---|---|---|---|---|---|
No. of isolates (%) | No. of spa types (%) | spa types (no. of isolates) | No. of isolates (%) | No. of spa types (%) | spa types (no. of isolates) | |
spa-CC002 | 9 | 3 (14) | t002 (4); t045 (2); t071 (3) | 10 | 4 (19) | t002 (5); t1215 (2); t18748 (1); t442 (2) |
spa-CC084 | 3 | 2 (10) | t084 (2); t491 (1); t19774 (1) | 5 | 2 (10) | t084 (3); t346 (2) |
spa cluster 3 | 3 | 2 (10) | t062 (2); t1399 (1) | 3 | 2 (10) | t062 (1); t2049 (2) |
spa cluster 4 | 9 | 2 (10) | t159 (1); t272 (8) | 2 | 1 (5) | t272 (2) |
spa cluster 5 | 12 | 2 (10) | t1476 (10); t1257 (2) | 10 | 2 (10) | t1476 (9); t18750 (1) |
spa cluster 6 | 3 | 1 (5) | t174 (3) | 13 | 2 (10) | t174 (12); t5471 (1) |
Singletons | 10 | 7 (33) | t015 (2); t148 (1); t2763 (1); t317 (3); t355 (1); t786 (1); t843 (1) | 13 | 7 (33) | t015 (2); t18354 (1); t1597 (1); t2078 (4); t335 (2); t881 (1); t891 (2) |
Unaligned/spa types with unknown repeat succession | 2 | 2 (10) | txAC (1) | 1 | 1 (5) | t15783 (1) |
Total | 51 | 21 | 57 | 21 |