title: 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.
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: B J
authors.initials: BJ
authors.lastname: Metcalf
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: S
authors.initials: S
authors.lastname: Chochua
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: R E
authors.initials: RE
authors.lastname: Gertz
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Z
authors.initials: Z
authors.lastname: Li
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: H
authors.initials: H
authors.lastname: Walker
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: T
authors.initials: T
authors.lastname: Tran
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: P A
authors.initials: PA
authors.lastname: Hawkins
authors.affiliation: Minnesota Department of Health, St Paul, MN, USA.
authors.forename: A
authors.initials: A
authors.lastname: Glennen
authors.affiliation: Minnesota Department of Health, St Paul, MN, USA.
authors.forename: R
authors.initials: R
authors.lastname: Lynfield
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Li
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: L
authors.initials: L
authors.lastname: McGee
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA. Electronic address: bbeall@cdc.gov.
authors.forename: B
authors.initials: B
authors.lastname: Beall
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D002701:Chloramphenicol / Q000494:pharmacology; D002939:Ciprofloxacin / Q000494:pharmacology; D002981:Clindamycin / Q000494:pharmacology; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D004917:Erythromycin / Q000494:pharmacology; D005798:Genes, Bacterial; D006801:Humans; D008826:Microbial Sensitivity Tests; D009154:Mutation; D046915:Penicillin-Binding Proteins / Q000235:genetics; D010406:Penicillins / Q000494:pharmacology; D011008:Pneumococcal Infections / Q000453:epidemiology* / Q000382:microbiology; D012338:RNA, Ribosomal, 23S / Q000235:genetics / Q000302:isolation & purification; D013296:Streptococcus pneumoniae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D013752:Tetracycline / Q000494:pharmacology; D015662:Trimethoprim, Sulfamethoxazole Drug Combination / Q000494:pharmacology; D014481:United States / Q000453:epidemiology
chemical_list: D000900:Anti-Bacterial Agents; D046915:Penicillin-Binding Proteins; D010406:Penicillins; D012338:RNA, Ribosomal, 23S; D002981:Clindamycin; D002939:Ciprofloxacin; D004917:Erythromycin; D002701:Chloramphenicol; D015662:Trimethoprim, Sulfamethoxazole Drug Combination; D013752:Tetracycline
keywords: Accessory genome; Core genome; Minimum inhibitory concentrations; Pneumococcal; Whole genome