Article Figures & Data
Figures
- FIG. 1.
Eighty-three clonal sets representing the isolates genotyped and the STs encountered in 1999, 2001, and 2002. Solid lines connect STs within the same clonal group determined by eBURST analysis. STs within the same eBURST group are indicated in boldface. Closely related outliers within the same clonal set are connected to eBURST sets by dotted lines. Numbers in red indicate STs calculated as founders by using eBURST with the STs generated from this study and also calculated as founders by using all known STs (28). Numbers in green indicate STs calculated as founders solely by using all known STs. Numbers in blue indicate STs calculated as founders by using only the STs found in this study for the analysis. Serotypes in parentheses indicate different serotype associations listed at www.mlst.net for the indicated STs. When no parentheses are indicated, no differences in serotype associations for the STs were observed between this study and www.mlst.net .
- FIG.2.
Clonal compositions of individual serotypes from invasive surveillance. The left, middle, and right columns represent isolates recovered in 1999, 2001, and 2002, respectively. The NPIs analyzed depict the numbers of isolates from individuals 5 years of age or older that were subjected to PFGE. The PIs analyzed depict the numbers of isolates from individuals less than 5 years of age that were subjected to PFGE. The percentages depict the proportions of invasive pneumococcal isolates within these serotypes that were subjected to genetic analysis. Where the numbers corresponding to these percentages are in parentheses, they refer to the total numbers of ABCs isolates within that age and serotype. The letter P indicates that at least 15% of the indicated clonal set within the indicated serotype were penicillin nonsusceptible. Serotypes in parentheses are shown when the serotype distributions listed in the global database (28) differed in any way from what we observed. Underlines indicate STs directly shared by PMEN clones (27) or clonal complexes containing these STs found among PMEN clones. Up to 30% of the isolates within a given serotype had unique PFGE profiles and were not subjected to MLST (represented by gaps in the columns). Such isolates could possibly belong to any of the clonal sets included or could represent additional clonal sets.
Tables
- TABLE 1.
Invasive pneumococcal disease incidence in 1999 and 2002a
Serotype(s) Age group (yr) 1999 2002 Change in rate P valuec No. of cases Rateb No. of cases Rate All <5 1,167 96.36 308 24.05 −72.31 <0.001 ≥5 3,141 19.08 2,418 13.72 −5.36 <0.001 All 4,308 24.37 2,726 14.42 −10.05 <0.001 PCV7 serogroups except 19A <5 1,064 87.85 143 11.16 −76.69 <0.001 ≥5 2,067 12.55 1,233 7.00 −5.55 <0.001 All 3,131 17.71 1,376 7.28 −10.43 <0.001 Non-PCV7 serogroups plus 19A <5 103 8.50 165 12.88 +4.38 <0.001 ≥5 1,067 6.48 1,185 6.72 +0.24 0.4 All 1,170 6.62 1,350 7.14 +0.52 0.06 ↵ a The surveillance areas included California (San Francisco only), Connecticut (state), Georgia (the 20-county Atlanta metro area), Maryland (the 7-county Baltimore II area), Minnesota (the 7-county Twin Cities area), New York (the 15-county Albany and Rochester areas), Oregon (the 3-county Portland area), and Tennessee (4 counties).
↵ b Number of cases per 100,000 individuals.
↵ c P values are for 1999 versus 2002.
- TABLE 2.
Incidence of invasive cases in group less than 5 years of age due to PCV7-nonrelated serotypes and serotype 19A in 2002 relative to incidence in 1999a
Serotype 1999 2002 P valued Actual (projectedb) no. of cases % of totalc Actual (projected) no. of cases % of total 1 6 (7) [0.6] 3 [1] 3 6 (7) [0.6] 8 (9) [2.9] 0.002 5 1 [<0.1] 0 7F 8 (9) [0.8] 11 (13) [4.2] <0.001 10A 1 [<0.1] 3 [1] 11A 1 [<0.1] 4 (5) [1.6] 12F 12 (14) [1.2] 7 (8) [2.6] 0.106 15B/15C/15F 6 (7) [0.6] 26 (30) [9.7] <0.001 16F 2 [<0.1] 2 [0.6] 17F 0 1 [0.3] 19A 20 (23) [2] 41 (47) [15.3] <0.001 22F 7 [0.6] 9 (10) [3.2] 0.002 24B/24F 1 [<0.1] 0 33A 0 1 [0.3] 33F 8 (9) [0.8] 14 (16) [5.2] <0.001 35B 2 [<0.1] 1 [0.3] 35F 0 1 [0.3] 38 5 (6) [0.5] 11 (13) [4.2] <0.001 Nontypeable 2 [<0.1] 0 Total 1,167 308 ↵ a The surveillance areas are the same as those listed in footnote a of Table 1.
↵ b Projected number of cases in the group <5 years of age for the indicated surveillance areas since serotypes were not determined for 171 of the total (n = 1,167) year 1999 isolates and were not determined for 41 of the the total (n = 308) year 2002 isolates.
↵ c Percentage of total isolates recovered from this age group in the indicated year.
↵ d Comparison of proportions for serotypes which have ≥2% of total strains in at least 1 year by using the chi-square or the Fisher exact test.
- TABLE 3.
PMEN clones sharing genetic identity or close genetic relatedness to ABCs pneumococcal isolates recovered in 1999, 2001, and 2002
PMEN clone (ST) Serotype(s) of invasive pneumococcal isolates genetically related to PMEN clonea 1999 2001 2002 Spain23F-1 (ST81) 19F, 23F, 14, 19A 19F, 23F 19A, 23F Spain6B-2 (ST90) 6B, 6A 6B Spain9V-3 (ST156) 9V, 6B, 14 9V, 14, 19F, 9A 15B, 9N Tennessee23F-4 (ST37) 23F 23F, 23A 23A Spain14-5 (ST18) 14 Hungary19A-6 (ST268) 23F South Africa6B-8 (ST185) 6B England14-9 (ST9) 14, 19F 14 Taiwan19F-14 (ST236) 19F 19F 19A Taiwan23F-15 (ST242) 23F 23F 23F Maryland6B-17 (ST384) 6B 6B Columbia5-19 (ST289) 5 5 Portugal19F-21 (ST177) 19F 19F North Carolina6A-23 (ST376) 6A 6A 6A, 19A Utah35B-24 (ST377) 35B 35B 35B Sweden15A-25 (ST63) 15A 15A, 14 Colombia23F-26 (ST338) 23A 23A ↵ a A total of 1,168 invasive isolates were examined from year 1999, 1,126 invasive isolates were examined from year 2001, and 377 invasive isolates were examined from year 2001.
- TABLE 4.
Clonal complex distribution among invasive pneumococcal isolates in 1999, 2001, and 2002
Serotype (clonal complex)a No. of isolates within complex/no. of isolates analyzed (%) in the following years for the indicated age groups 1999 2001 2002b <5 yr ≥5 yr <5 yr ≥5 yr <5 yr ≥5 yr 1 (ST227) 5/6 (83.3) 15/15 (100) 4/4 (100) 28/34 (82.4) 4/4 (100) None analyzed 1 (ST217) 1/6 (16.7) 0/15 0/4 1/34 (2.9) 0/4 None analyzed 1 (ST1174) 0/6 0/6 0/6 2/34 (5.9) 0/4 None analyzed 3 (ST180) 6/6 (100) 48/50 (96.0) 6/6 (100) 68/70 (97.0) 8/8 (100) 11/11 (100) 4 (CC899) 53/71 (74.6) None analyzed 29/35 (82.9) 18/34 (52.9) None analyzed 1/1 (100) 4 (ST205) 8/71 (11.3) None analyzed 6/35 (17.1) 11/34 (32.4) None analyzed 0/1 (0) 5 (ST653) 100 (1) None analyzed 1/1 (100) 1/1 (100) No type 5s None analyzed 6A (CC1296) 19/57 (33.3) 0/1 10/38 (26.3) 0/9 4/13 (30.7) 14/41 (34.1) 6A (CC460) 13/57 (22.4) 0/1 11/38 (29.4) 3/9 (33.3) 3/13 (23.1) 0/41 6A (CC473) 5/57 (8.8) 0/1 7/38 (18.4) 1/9 (11.1) 1/13 (7.7) 15/41 (36.6) 6A (ST395) 1/57 (1.8) 1/1 (100) 3/38 (7.9) 0/9 3/13 (23.1) 2/41 (4.9) 6A (CC490) None detectedb 0/1 2/38 (5.3) 0/9 None detected None detected 6A (CC138) None detected 0/1 2/38 (5.3) 0/9 None detected None detected 6A (ST1091) None detected 0/1 1/38 (2.6) 0/9 None detected None detected 6A (ST1175) None detected 0/1 1/38 (2.6) 0/9 None detected None detected 6A (ST90) 1/57 (1.8) 0 None detected 0/9 None detected None detected 6A (ST660) 1/57 (1.8) 0 None detected 0/9 None detected None detected 6A (ST690) None detected 0 None detected 2/9 (22.2) None detected None detected 6A (CC1292) None detected 0/1 None detected 3/9 (33.3) None detected 6/41 6B (CC138) 13/103 (12.6) 0/1 13/45 (28.9) 2/15 (9.1) None analyzed 1/4 (25.0) 6B (CC146) 22/103 (21.4) 0/1 11/45 (24.4) 4/15 (28.6) None analyzed 0/4 6B (ST90) 13/103 (12.6) 0/1 13/45 (28.9) 5/15 (28.6) None analyzed 0/4 6B (CC384) 6/103 (5.8) 0/1 5/45 (11.1) 3/15 (20.0) None analyzed 0/4 6B (CC1269) 3/103 (2.9) 0/1 None detected 0/15 None analyzed 0/4 6B (CC490) None detected 0/1 2/45 (4.4) 0/15 None analyzed 3/4 (75.0) 6B (ST185) 1/103 (1.0) 0/1 None detected 0/15 None analyzed 0/4 6B (ST690) None detected 1/1 None detected 1/15 (6.7) None analyzed 0/4 7B (ST664) 1/1 (100) No type 7Bs No type 7Bs No type 7Bs No type 7B No type 7Bs 7C (ST1207) No type 7C No type 7Cs No type 7Cs 1/1 (100) 1/1 (100) 1/1 (100) 7F (ST191) 7/7 (100) 22/24 (91.7) 13/15 (86.7) 29/30 (96.7) 5/6 (83.3) 3/3 (100) 7F (CC218) 0/7 1/24 (4.2) None detected None detected None detected 0/3 8 (ST53) No type 8 None analyzed 2/2 (100) 1/10 (10.0) No type 8 100 (1) 8 (ST1268) No type 8 None analyzed 0/2 9/10 (90.0) No type 8 0/1 9A (CC156) No type 9A No type 9As 3/3 (100) No type 9As No type 9A No type 9As 9N (CC66) 2/2 (100) 9/11 (81.8) 3/3 (100) 34/37 (91.9) None analyzed 3/5 (60.0) 9N (CC156) 0/2 None detected 0/3 None detected None analyzed 1/5 (20.0) 9N (CC1257) 0/2 None detected 0/3 None detected None analyzed 1/5 (20.0) 9V (CC156) 60/72 (83.3) 21/26 (80.1) 26/38 (68.4) 28/42 (66.7) 2/2 (100) 7/7 (100) 9V (CC1269) 9/72 (12.5) 3/26 (11.5) 11/38 (28.9) 14/42 (33.3) 0/2 0/2 10A (CC460) 1/1 (100) None analyzed 3/3 (100) 2/5 (40) 3/3 (100) 2/2 (100) 10A (ST1263) 0/1 None analyzed 0/3 2/5 (40) 0/3 0/2 11A (CC62) 1/1 (100) 22/24 (87.5) 5/5 (100) 41/41 (100) 2/2 (100) 9/9 (100) 12F (CC218) 11/11 (100) 48/49 (97.8) 17/17 (100) 65/65 (100) 4/6 (66.7) 1/1 (100) 12F (ST989) 0/11 None detected 0/17 0/65 1/6 (16.7) 0/1 12F (CC1292) 0/11 None detected 0/17 0/65 1/6 (16.7) 0/1 13 (CC392) No type 13 None analyzed No type 13s 2/2 (100) No type 13 0/1 13 (ST1260) No type 13 None analyzed No type 13s 0/2 No type 13 1/1 (100) 14 (CC13) 96/208 (46.2) None analyzed 48/91 (52.7) 19/36 (52.7) None analyzed 3/3 (100) 14 (CC124) 78/208 (37.5) None analyzed 33/91 (30.0) 9/36 (25.0) None analyzed 0/3 14 (CC63) None detected None detected 6/91 (6.6) 0/36 None analyzed 0/3 14 (CC1269) 5/208 (2.4) None analyzed 2/91 (2.2) 2/36 (5.9) None analyzed 0/3 14 (CC156) None detected None analyzed 3/91 (3.3) 1/36 (2.8) None analyzed 0/3 14 (CC66) 4/208 (1.9) None analyzed 1/91 (1.1) 1/36 (2.8) None analyzed 0/3 15A (CC63) No type 15As None analyzed No type 15As 3/3 (100) No type 15As 12/13 (92.3) 15A (ST817) No type 15As None analyzed No type 15As 0/3 No type 15As 1/13 (7.7) 15BC (CC199) 6/6 (100) None analyzed 20/22 (90.9) 3/3 (100) 27/33 (81.8) 5/5 (100) 15BC (ST1262) 0/6 None analyzed None detected 0/3 2/33 (6.1) 0/5 15BC (ST1267) 0/6 None analyzed None detected 0/3 2/33 (6.1) 0/5 15BC (ST1259) 0/6 None analyzed None detected 0/3 1/33 (3.0) 0/5 15BC (CC156) 0/6 None analyzed None detected 0/3 1/33 (3.0) 0/5 16F (CC659) 1/1 (100) 0/2 No type 16Fs 7/7 (100) 2/2 (100) 1/3 (33.3) 16F (CC30) 0/1 2/2 (100) No type 16s 0/7 0/2 2/3 (66.7) 17F (CC392) No type 17F None analyzed 1/1 (100) None analyzed 1/1 (100) None analyzed 18BCF (CC113) 74/93 (79.6) None analyzed 28/40 (68.3) 9/11 (81.8) 2/3 (66.7) 2/2 (100) 18BCF (ST496) 8/93 (8.6) None analyzed 5/40 (12.5) 1/11 (9.0) 0/3 0/2 18BCF (ST666) 1/93 (1.1) None analyzed 1/40 (2.4) 1/11 (9.0) 1/3 (33.3) 0/2 18BCF (CC66) 1/93 (1.1) None analyzed None detected 0/11 0/2 0/2 19A (ST199) 13/18 (72.2) 46/64 (71.9) 18/29 (62.1) 10/10 (100) 27/40 (67.5) 32/45 (71.1) 19A (CC172) None detected 2/64 (3.1) 2/29 (6.9) 0/10 0/40 1/45 (2.2) 19A (ST665) 1/18 (5.5) None detected 1/29 (3.4) None detected 0/40 0/45 19A (CC236) None detected None detected 1/29 (3.4) None detected 3/40 (7.5) 1/45 (2.2) 19A (CC1296) None detected None detected None detected None detected 4/40 (10.0) 5/45 (11.1) 19A (CC81) 1/18 (5.5) None detected None detected None detected 1/40 (2.5) 2/45 (4.4) 19A (ST230) None detected None detected 2/29 (6.9) None detected 0/40 0/45 19A (ST1297) None detected None detected 1/29 (3.4) None detected 3/40 (7.5) 2/45 (4.4) 19A (CC62) None detected None detected None detected None detected 2/40 (5.0) 0/45 19A (ST1374) None detected None detected None detected 0/10 0/40 1/45 (2.2) 19A (ST847) None detected None detected None detected 0/10 0/40 1/45 (2.2) 19F (CC236) 23/110 (20.9) None examined 10/47 (21.3) 3/12 (25.0) 1/2 (50) 8/9 (88.9) 19F (CC251) 22/110 (20.0) None examined 19/47 (40.4) 3/12 (25.0) 0/2 0/9 19F (CC81) 13/110 (11.8) None examined 3/47 (6.4) 3/12 (25.0) 0/2 0/9 19F (CC199) 10/110 (9.1) None examined 1/47 (2.1) 1/12 (9.1) 0/2 0/9 19F (ST655) 2/110 (1.8) None examined 0/47 0/12 0/2 0/9 19F (CC177) 2/110 (1.8) None examined 4/47 (8.5) 0/12 0/2 0/9 19F (CC1269) 1/110 (0.9) None examined 2/47 (4.3) 1/12 (9.1) 0/2 0/9 19F (ST1340) None detected None examined 0/47 0/12 1/2 (50) 0/9 19F (CC13) 1/110 (0.9) None examined 0/47 0/12 0/2 0/9 19F (ST43) 1/110 (0.9) None examined 4/47 (8.5) 0/12 0/2 0/9 19F (CC172) None detected None examined 1/47 (2.1) 0/12 0/2 0/9 19F (CC425) 4/110 (3.6) None examined 3/47 (6.4) 0/12 0/2 0/9 19F (CC63) None detected None examined 0/47 1/12 (9.1) 0/2 0/9 19F (ST1203) None detected None examined 0/47 0/12 0/2 1/9 (11.1) 20 (CC899) No type 20 None examined 1/1 (100) 4/6 (66.7) No type 20 None examined 20 (CC1257) No type 20 None examined 0/1 33.3 (2) No type 20 None examined 22F (CC433) 6/6 (100) 30/31 (96.8) 19/19 (100) 90.2 (46) 92.9 (13) 100 (2) 22F (ST1294) 0/2 None detected 0/1 None detected 7.1 (1) 0/2 23A (CC172) 2/2 (100) None examined 0/1 0/1 No type 23A 5/6 (83.3) 23A (ST1336) 0/2 None examined 1/1 (100) 0/1 No type 23A 0/6 23A (ST1338) 0/2 None examined 0 2/4 (50.0) No type 23A 0/6 23A (CC37) 0/2 None examined 0 2/4 (50.0) No type 23A 1/6 (16.7) 23F (CC37) 46/64 (71.9) None examined 26/37 (70.3) 6/13 (46.2) None examined 0/5 23F (CC81) 11/64 (17.2) None examined 5/37 (13.5) 4/13 (30.7) None examined 4/5 (80.0) 23F (ST242) 4/64 (6.2) None examined 1/37 (2.7) 2/13 (15.4) None examined 1/5 (20.0) 23F (CC662) 1/64 (1.6) None examined None detected 0/13 None examined 0/5 23F (CC268) None detected None examined 1/37 (2.7) 1/13 (7.7) None examined 0/5 23F (CC460) None detected None examined 2/37 (5.4) 0/13 None examined 0/5 24BF (CC72) No type 24BF None examined 1/1 (100) None examined None examined 1/1 (100) 28F (ST546) No type 28F No type 28F No type 28F No 28F isolates No 28F isolates 100 (1) 31 (ST568) No type 31 1/1 (100) No type 31 2/2 (100) 1/1 (100) No type 31 33F (CC662) 7/7 (100) 1/1 (100) 10/11 (90.9) 7/8 (87.5) 18/18 (100) 1/1 (100) 33F (ST1012) 0/7 0/1 1/11 (9.1) 1/8 (12.5) 0/18 0/1 35B (CC377) 2/2 (100) 10/14 (71.4) 2/2 (100) 27/35 (77.1) 100 (1) 18/19 (94.7) 35B (ST452) 0/2 4/14 (28.6) 0/2 8/35 (22.9) 0/1 1/19 (5.3) 35F (ST498) No type 35F None examined 2/2 (100) 2/2 (100) None examined None examined 37 (ST447) No type 37 None examined No type 37 None examined No type 37 1/2 (50.0) 38 (ST393) 5/5 (100) None examined 7/7 (100) 1/1 (100) 15/15 (100) None examined ↵ a Clonal complexes in boldface were found only among isolates from individuals ≥5 years of age. Up to 30% of the isolates within a given serotype had unique PFGE profiles and were not subjected to MLST (represented by gaps in the columns in Fig. 2). Such isolates could possibly belong to any of the clonal sets included or could represent additional clonal sets.
↵ b Year 2002 isolates were primarily selected from non-PCV7 serotypes.
