Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States

Abstract

Our whole genome sequence (WGS) pipeline was assessed for accurate prediction of antimicrobial phenotypes. For 2316 invasive pneumococcal isolates recovered during 2015 we compared WGS pipeline data to broth dilution testing (BDT) for 18 antimicrobials. For 11 antimicrobials categorical discrepancies were assigned when WGS-predicted MICs and BDT MICs predicted different categorizations for susceptibility, intermediate resistance or resistance, ranging from 0.9% (tetracycline) to 2.9% (amoxicillin). For β-lactam antibiotics, the occurrence of at least four-fold differences in MIC ranged from 0.2% (meropenem) to 1.0% (penicillin), although phenotypic retesting resolved 25%-78% of these discrepancies. Non-susceptibility to penicillin, predicted by penicillin-binding protein types, was 2.7% (non-meningitis criteria) and 23.8% (meningitis criteria). Other common resistance determinants included mef (475 isolates), ermB (191 isolates), ermB + mef (48 isolates), tetM (261 isolates) and cat (51 isolates). Additional accessory resistance genes (tetS, tet32, aphA-3, sat4) were rarely detected (one to three isolates). Rare core genome mutations conferring erythromycin-resistance included a two-codon rplD insertion (rplD69-KG-70) and the 23S rRNA A2061G substitution (six isolates). Intermediate cotrimoxazole-resistance was associated with one or two codon insertions within folP (238 isolates) or the folA I100L substitution (38 isolates), whereas full cotrimoxazole-resistance was attributed to alterations in both genes (172 isolates). The two levofloxacin-resistant isolates contained parC and/or gyrA mutations. Of 11 remaining isolates with moderately elevated MICs to both ciprofloxacin and levofloxacin, seven contained parC or gyrA mutations. The two rifampin-resistant isolates contained rpoB mutations. WGS-based antimicrobial phenotype prediction was an informative alternative to BDT for invasive pneumococci.

Spread of Meropenem-ResistantStreptococcus pneumoniaeSerotype 15A-ST63 Clone in Japan, 2012–2014

“…We allocated PBP transpeptidase type numbers to these contigs by using previous PBP sequence data from the United States ( 5 , 29 – 31 ). To predict a causal PBP transpeptidase type for meropenem resistance in serotype 15A-ST63 isolates from Japan, we identified recombination sites within these serotype 15A isolates by using Gubbins.…”

Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015

“…Determination of PBP2x transpeptidase sequence types (STs) of group B streptococci (GBS) and pneumococci is a very sensitive mechanism for detecting potential first-step mutations conferring decreased susceptibility or intermediate resistance to penicillin and other ␤-lactam antibiotics (16)(17)(18). We used this same approach with the corresponding PBP2x region from S. pyogenes.…”

“…GAS chromosomal DNA preparation, library construction, and WGS generation for the 1,454 isolates were performed as previously described (16).…”

Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

“…In general, Tn916 positive isolates exhibited highlevel resistance to tetracycline, clindamycin, and erythromycin. However, three USA strains were susceptible to macrolides as the result of a previously described ermBS marker, a missense substitution within ermB that is associated with erythromycin and clindamycin-susceptibility [52]. Additional phylogenetic analysis of 26 core transposon clusters of orthologous genes (COGs) as well as genealogies of Int-Tn, ermB, and tetM illustrated that there were in fact two acquisitions of genetically similar Tn916 transposons among Clade II isolates (Supplemental Figure 8).…”