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Volume 23, Number 6—June 2017

Research

Invasive Serotype 35B Pneumococci Including an Expanding Serotype Switch Lineage, United States, 2015–2016

Sopio Chochua, Benjamin J. Metcalf, Zhongya Li, Hollis Walker, Theresa Tran, Lesley McGee, and Bernard BeallComments to Author 
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA

Main Article

Table 1

WGS pipeline features of 199 invasive serotype 35B pneumococcal isolates, United States, 2015–2016 and 2 35B ST156 lineage isolates obtained during 2009 and 2012*

CC (no.)† ST No. PBP type‡ Non- PBP resistance determinants§ Antimicrobial resistance phenotype, μg/mL¶
States
Pen Amo Tax Cft Cfx Mer Ery Cli + Tet Cot Fq#
156 (21) 156 15** 4:12:7 mef, folAI100L, folPins178 2 4 1 1 >2 1 R S R S CT, GA, MN, NY, TN, MD
10174 1†† 4:7:18 mef, folAI100L, folPins178 2 1 1 1 >2 0.5 R S R S NM
11584 2 4:12:7 mef, folAI100L, folPins178 2 4 1 1 >2 1 R S R S TN
9910 1 4:12:7 mef, folAI100L, folPins178 2 4 1 1 >2 1 R S R S TN
162 1 0:0:0 None <0.03 <0.03 <0.06 <0.03 <0.5 <0.06 S S S S NM
12921 1 4:11:7 mef, folAI100L, folPins178 2 8 1 1 >2 1 R S R S TN
63 (1) 11818 1 4:31:114 ermB, tetM, folPins195 1 4 1 0.5 >2 0.5 R R I S MD
1092 (1) 1092 1 6:7:36 folAI100L, folPins195 1 1 0.5 1 >2 0.25 S S R S NM
452 (10) 452 8 0:0:0 None <0.03 <0.03 <0.06 <0.03 <0.5 <0.06 S S S S CA, CT, NM, OR
452 1 0:0:0 mef <0.03 <0.03 <0.06 <0.03 <0.5 <0.06 R S S S MD
452 1 0:0:148 None 0.06 ≤0.03 0.12 0.12 <0.5 <0.06 S S S S CO
558 (168) 558 104 4:7:7 mef 2 4 1 1 >2 0.5 R S S S CA, CO, CT, GA,MD,MN, NM, NY, TN
558 1 4:7:7 mef, ParC-D83Y, GyrA-S81Y 2 4 1 1 >2 0.5 R S S R TN
558 1 4:7:7 mef, ParC-D83Y 2 4 1 1 >2 0.5 R S S I MD
558 1 4:7:7 mef, ParC-S79F 2 4 1 1 >2 0.5 R S S I CT
558 1 4:7:7 mef, folPins186 2 4 1 1 >2 0.5 R S I S CA
558 22 4:7:7 None 2 4 1 1 >2 0.5 S S S S CA, CO, CT, GA, MD, MN, NM,TN
558 2 4:7:7 folAI100L 2 4 1 1 >2 0.5 S S I S GA, MD
558 1 4:7:7 folPins173 2 4 1 1 >2 0.5 S S I S TN
558 1 4:7:7 folPins189 2 4 1 1 >2 0.5 S S I S MD
558 1 4:7:7 folPins195 2 4 1 1 >2 0.5 S S I S NM
558 1 4:7:7 folAI100L, folPins180 2 4 1 1 >2 0.5 S S R S CO
558 1 4:7:7 folAI100L, folPins169 2 4 1 4 >2 0.5 S S R S CO
558 1 4:7:28 mef 0.12 <0.03 <0.06 0.06 <0.5 <0.06 R S S S CO
558 1 4:7:112 mef 2 2 1 1 >2 0.5 R S S S TN
558 1 4:7:133 mef 2 2 1 1 >2 0.5 R S S S GA
558 2 4:120:7 mef 2 4 1 1 >2 1 R S S S CT
558 1 4:123:7 mef 2 4 1 1 >2 0.5 R S S S NY
558 1 102:7:7 mef 2 2 1 1 >2 0.5 R S S S CT
558 1 106:7:7 None 1 1 0.5 0.5 >2 0.5 S S S S MD
558 1 4:135:7 folAI100L, folPins169 2 4 1 4 >2 0.5 S S R S CO
558 1 4:139:7 mef 2 4 1 4 >2 0.5 R S S S MN
6961 1 4:7:7 None 2 4 1 1 >2 0.5 S S S S MD
7486 1 4:7:7 mef 2 4 1 1 >2 0.5 R S S S TN
7487 1 4:49:7 None 2 8 1 1 >2 1 S S S S CT
10493 6 4:7:7 mef 2 4 1 1 >2 0.5 R S S S CT, GA, MD, NM
10493 1 4:7:7 mef, folAI100L 2 4 1 1 >2 0.5 R S I S NM
11250 1 4:14:7 folPins169 2 8 1 1 >2 1 S S I S GA
11254 2 4:7:7 folAI100L, folPins169 2 4 1 1 >2 0.5 R S R S CO, MD
11603 1 4:7:7 mef 2 4 1 1 >2 0.5 R S S S CT
11604 1 4:7:7 mef 2 4 1 1 >2 0.5 R S S S MD
11606 1 4:7:7 None 2 4 1 1 >2 0.5 S S S S CO
11866 1 4:7:7 mef 2 4 1 1 >2 0.5 R S S S GA
12854 1 4:7:7 mef 2 4 1 1 >2 0.5 R S S S GA
12883 1 4:7:7 20L 2 4 1 1 >2 0.5 S S I S MN
12885 1 4:7:7 mef 2 4 1 1 >2 0.5 R S S S CT
12922 1 4:142:7 None 4 8 1 2 >2 >1 S S S S MD

*All isolates were positive for pilus PI-type 1 and negative for pilus PI-type 2. CC, clonal complex; I, intermediate resistance; MLST, multilocus sequence type; PBP, penicillin-binding protein; R, resistant; S, susceptible; ST, sequence type; WGS, whole-genome sequencing.
†CCs that probably arose through serotype switching are indicated in bold.
‡MIC correlates for PBP types (http://www.cdc.gov/streptlab/mic-tables.html (15). Variant PBPs potentially contributing to increased MICs relative to 4:7:7 or 0:0:0 are indicated in bold. Three isolates yielded only partial PBP types because of genomic assembly error, but were assigned PBP type 4:7:7 because of partial identity and consistent phenotypic β-lactam MIC profile.
§For a description of WGS-based bioinformatic pipeline for deduction of all features shown, see Gertz et al (4) and Desai et al. (7). For a description of folP insertions (folPins169), see Figure 1 in Gertz et al. (4).
¶Predicted MICs for β-lactam antimicrobial drugs were based on transpeptidase domain sequences of PBPs 1a, 2b, and 2x (http://www.cdc.gov/streplab/mic-tables.html). For penicillin (meningitis only), nonsusceptible is considered >0.12 μg/mL (16). Currently applied clinical cutoffs are also provided for the other 5 β-lactams shown (16). Where shown, I, R, and S correspond to breakpoint MIC values (16). Increased MICs potentially attributable to PBP type alterations are indicated in bold. Amo, amoxicillin; Cft, ceftriaxone; Cfx, cefuroxime; Cli, clindamycin; Cot, cotrimoxazole; Ery, erythromycin; Fq, fluoroquinolones levofloxacin and ciprofloxacin; Mer, meropenem; Pen, penicillin; Tax, cefotaxime.
#MIC of 4 μg/mL for ciprofloxacin is considered intermediate resistance.
**Includes single putative progenitor strain (2012221165) isolated from a 4-y-old child during 2012 (Figure 2).
††2009219987 was isolated from an infant in New Mexico during 2009 (Figure 2).

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