Supplementary Table 1. Population characteristics for the different vaccination groups. PCV vaccination groups PCV at 0, 1 & 2m PCV at 1, 2 & 3m No PCV (neonatal) (infant) (control) P-value Pneumococcal carriage ≤ 2 wks, % pos 39% (35/89) 40% (39/97) 40% (37/93) 0.993 Gravida, % primigravida 22% (19/85) 36% (34/95) 32% (29/93) 0.137 9% (7/80) 5% (4/85) 13% (11/86) 0.174 Maternal Spn carriage a, % pos 36% (28/78) 31% (24/78) 22% (17/77) 0.163 Gender, % female 58% (52/89) 43% (42/97) 37% (59/93) 0.010 Gestation age (weeks; mean and IQR) 40.0 (39.0-40.0) 40.0 (39.0-40.0) 40.0 (39.0-40.0) 0.558 3.3 (3.0-3.6) 3.3 (3.0-3.5) 3.3 (3.0-3.6) 0.657 Maternal smoking pregnancy, % pos Birth weight (kg; mean and IQR) Maternal CbpA-IgG (AU/ml; mean and IQR) 7054 (3702-8925) 4919 (3270-7385) 5712 (2884-8056) 0.189 Maternal Ply-IgG (AU/ml; mean and IQR) 4487 (2755-8724) 4091 (2638-9216) 3818 (1733-8684) 0.790 Maternal PspA1-IgG (AU/ml; mean and IQR) 1297 (733-2767) 1414 (902-2048) 1821 (756-3102) 0.491 1 Maternal PspA2-IgG (AU/ml; mean and IQR) 3295 (1468-6194) 4481 (1460-7648) 3756 (2165-7811) 0.388 CbpA-IFN (pg/ml ; mean and IQR) 12 (2-398) 55 (25-244) 43 (9-112) 0.648 CbpA-IL5 2 (2-7) 2 (2-9) 2 (2-6) 0.691 CbpA-IL9 2 (2-7) 2 (2-8) 2 (2-7) 0.422 CbpA-IL10 8 (4-22) 8 (2-21) 8 (4-13) 0.939 CbpA-IL13 14 (6-17) 15 (6-28) 11 (2-21) 0.155 CbpA-TNF 6 (3-17) 6 (4-28) 6 (3-13) 0.373 Ply-IFN (pg/ml; mean and IQR) 48 (6-219) 25 (3-116) 33 (10-168) 0.534 Ply-IL5 2 (2-6) 2 (2-2) 2 (2-6) 0.213 Ply-IL9 5 (2-15) 3 (2-11) 5 (2-8) 0.818 Ply-IL10 10 (4-31) 4 (2-22) 11 (4-22) 0.206 Ply-IL13 9 (4-18) 10 (2-17) 8 (4-15) 0.720 Ply-TNF 6 (2-20) 5 (2-18) 10 (2-23) 0.940 70 (17-435) 0.566 PspA-IFN (pg/ml; mean and IQR) 93 (13-696) 118 (27-821) 2 PspA-IL5 4 (2-24) 5 (2-11) 5 (2-17) 0.793 PspA-IL9 4 (2-24) 4 (2-7) 4 (2-8) 0.769 PspA-IL10 11 (6-34) 9 (6-20) 10 (5-23) 0.880 PspA-IL13 24 (12-57) 23 (15-37) 24 (10-70) 0.811 PspA-TNF 4 (2-18) 8 (2-16) 4 (2-9) 0.285 CRM197-IFN (pg/ml; mean and IQR) 178 (21-661) 115 (33-933) 16 (2-1.87) <0.001 CRM197-IL5 36 (9-135) 56 (10-155) 2 (2-29) <0.001 CRM197-IL9 2 (2-8) 2 (2-14) 2 (2-4) 0.015 CRM197-IL10 2 (2-4) 2 (2-7) 2 (2-4) 0.417 20 (2-49) <0.001 2 (2-2) 0.077 CRM197-IL13 CRM197-TNF 77 (26-141) 2 (2-2) 89 (30-234) 2 (2-4) Children were randomized to receive 3 doses of a pneumococcal conjugate vaccine starting at birth (neonatal PCV), at 1 month of age or no PCV at all. Maternal Spn carriage (a) is nasopharyngeal carriage of S. pneumoniae (Spn) by the mother at the time of delivery. Maternal serum antibody titers were assessed as a surrogate marker for maternally-transferred antibody titers in the infants [12]. In vitro PBMC cytokine 3 responses to the pneumococcal proteins choline binding protein A (CbpA), pneumococcal surface protein A (PspA; family 1 and 2) and pneumolysin (Ply), and the study vaccine protein carrier CRM197 were determined at 9 months of age. . 4