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. 2020 Jan 29;5(1):e00969-19. doi: 10.1128/mSphere.00969-19

TABLE 1.

Isolates and their characteristicsa

Strain or isolate Reference Yr of isolation Site of origin Phenotypic resistanceb
 WGS cladec MLSTd
 Serotypee PBP3 resistance
 ftsI typeh Acquired resistance gene(s)i Mobile genetic element
Beta-lactam(s) Other agent(s) CC ST Levelf Groupf Typeg
0 11 1983 Blood A Te, Ch VI 6 119 Hib sPBP3 sPBP3 z alpha-x blaTEM-1, catP, tet(B) Tn6687
A 24 2007 Ear Cf Tx IV 57 57 NT Low II A lambda-2 — —
B 24 2007 Npxj Cf — V 3 367 NT Low II A lambda-2 — —
C 24 2007 Ear Cf — V 12 12 NT Low II H gamma — —
D 24 2007 Npx Cf — IV 422 411 NT Low II H gamma — —
E 20 2010 Eye A, Ac, Cf, Ct, Cx Tx, Ci IV 422 422 NT High III-like+ 3 ftsI-4 blaTEM-1 Tn6685
F 20 2013 Sputum A, Ac, Cf, Ct, Cx Tx, Te, Ch II 503 1282 NT High III-like+ 3 ftsI-4 blaTEM-1, catA-like, tet(B) Tn6686
G 20 2013 Sputum A, Ac, Cf, Ct, Cx Tx, Te, Ch, Ci II 503 159 NT High III+ 2 ftsI-5 blaTEM-1, catA-like, tet(B) Tn6686
G2 20 2013 Eye A, Ac, Cf, Ct, Cx Tx, Te, Ch, Ci II 503 159 NT High III+ 2 ftsI-5 blaTEM-1, catA-like, tet(B) Tn6686
G3 20 2013 Npx A, Ac, Cf, Ct, Cx Tx, Te, Ch, Ci II 503 159 NT High III+ 2 ftsI-5 blaTEM-1, catA-like, tet(B) Tn6686
H 20 2013 Npx A, Ac, Cf, Ct, Cx Tx V 245 836 NT High III+ 2 ftsI-2 blaTEM-1 pHblaTEM-1
I 20 2012 Ear A, Ac, Cf, Ct, Cx — I 124 124 Hif High III+ 2 ftsI-2 — —
a

Shading indicates identical resistance-conferring ftsI alleles or MGE shared by different strains or isolates.

b

A, ampicillin; Ac, amoxicillin-clavulanic acid; Cf, cefuroxime; Ct, cefotaxime; Cx, ceftriaxone; Tx, co-trimoxazole; Te, tetracycline; Ch, chloramphenicol; Ci, ciprofloxacin; —, none. For MICs and clinical breakpoints, see Table S2 in the supplemental material.

c

Whole-genome phylogeny with assignment to phylogenetic groups according to De Chiara et al. (50).

d

MLST, multilocus sequence typing; CC, clonal complex (named after predicted founder by eBURST analysis); ST, sequence type.

e

Hib, serotype b; Hif, serotype f; NT, nontypeable.

f

Based on amino acid substitutions in penicillin-binding protein 3 (PBP3), positions 385, 389, 517, and 526. sPBP3, no substitutions; Low, N526K or R517H; High, S385T in addition to N526K or R517H; II, N526K; III-like+, S385T, L389F, R517H; III+, S385T, L389F, N526K (20, 24).

g

Based on amino acid sequences in positions 350, 357, 377, 385, 389, 502, 517, 526, 532, 547, 557, 562, and 569 (substitutions underlined): z, DSMSLARNTVYVN (identical to the reference sequence Rd KW20 [53]); A, NSISLVRKTIYVS; H, DSMSLVRKTVYVN; 3, NNITFAHNSIHVS; 2, NNITFARKTIYLS (20, 24).

h

Based on partial nucleotide sequences in the transpeptidase domain of the ftsI gene (nt 1010 to 1719) (20, 24). The ftsI type for strain 0 clusters with Rd KW20 in group alpha (24) and is therefore assigned alpha-x.

i

bla, beta-lactamase gene; catA and catP, chloramphenicol resistance genes; tet(B), tetracycline resistance gene; —, none.

j

Npx, nasopharynx.