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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

2016; Elsevier BV; Volume: 22; Issue: 12 Linguagem: Inglês

10.1016/j.cmi.2016.08.001

1469-0691

Benjamin J. Metcalf, Sopio Chochua, Robert E. Gertz, Zheng Li, Hollis Walker, Theresa Tran, Paulina A. Hawkins, Anita Glennen, Ruth Lynfield, Y. Li, Lesley McGee, Bernard Beall, Arthur Reingold, Shelise Brooks, H. Randel, L. L. Miller, Brad J. White, Deborah Aragon, Meghan Barnes, J. Sadlowski, Susan Petit, Matthew Cartter, Carolina Márquez, Michael Wilson, M. Farley, Sabu Thomas, Amy Tunali, Wendy Baughman, Lee H. Harrison, Jonathan L. Benton, T. Carter, Rosemary Hollick, King K. Holmes, Andrea N. Riner, Corinne Holtzman, Richard Danila, K. MacInnes, Karen Scherzinger, K. Angeles, Joseph Bareta, L. O. Butler, S. Khanlian, Richard A. Mansmann, Megin Nichols, Nancy M. Bennett, Shelley M. Zansky, Salvatore Currenti, Suzanne McGuire, Ann Thomas, Malthe Schmidt, Jessica Thompson, Tasha Poissant, William Schaffner, B. Barnes, Katja Leib, Kelly A. Dyer, Laura E. McKnight, Ryan Gierke, Olivia Almendares, J. B. Hudson, Londell McGlone, Gayle Langley,

Antimicrobial Resistance in Staphylococcus

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.