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Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA

2017; Elsevier BV; Volume: 23; Issue: 8 Linguagem: Inglês

10.1016/j.cmi.2017.02.021

1469-0691

Ben J. Metcalf, Sopio Chochua, Robert E. Gertz, Paulina A. Hawkins, Jessica N. Ricaldi, Zheng Li, Hollis Walker, Theresa Tran, Joan Rivers, Saundra Mathis, Delois Jackson, Anita Glennen, Ruth Lynfield, 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, Olivia Almendares, J. B. Hudson, Londell McGlone, Cynthia G. Whitney, Stephanie J. Schrag, Gayle Langley,

Streptococcal Infections and Treatments

ObjectivesOur objective was to evaluate and exploit a whole genome sequence (WGS) bioinformatics pipeline for predicting antimicrobial resistance and capsular serotypes from invasive group B streptococci (iGBS).MethodsFor 1975 iGBS recovered during 2015 from CDC's Active Bacterial Core surveillance, we compared pipeline predictions with broth dilution testing. Fifty-six isolates from earlier surveillance were included for testing β-lactams. Conventional serotyping was compared to WGS-based assignments for 302 isolates.ResultsAll 28 isolates with reduced susceptibility to β-lactam antibiotics harboured one of 19 rare PBP2x types. Resistances to erythromycin/clindamycin (808/1975 isolates, 41.0%), erythromycin (235/1975, 11.9%) and lincosamide/streptogramin A/pleuromutilins (56/1975, 2.8%) were predicted by the presence of erm-methylase, mef and lsa determinants, respectively (41 of 56 lsa gene-positive isolates also contained lnu, erm and/or mef genes). Presence of both erm and lsa determinants (25 isolates) predicted non-susceptibility to quinupristin/dalfopristin. Most isolates (1680/1975, 85.1%) were tet gene-positive, although 41/1565 (2.6%) tetM-positive isolates were tetracycline-susceptible. All 53 fluoroquinolone-resistant isolates contained ParC and/or GyrA substitutions. Resistances to rifampin (eight isolates), trimethoprim, chloramphenicol and vancomycin (two isolates each) were predicted by the pipeline. Resistance to macrolides/lincosamides without pipeline prediction was rare and correlated to divergent resistance genes or rRNA A2062G substitution. A selection of 267 isolates assigned WGS-based serotypes were also conventionally serotyped. Of these, 246 (92.1%) were in agreement, with the remaining 21 (7.8%) conventionally non-serotypeable. For 32 of 1975 isolates (1.6%), WGS-based serotypes could not be assigned.ConclusionThe WGS-based assignment of iGBS resistance features and serotypes is an accurate substitute for phenotypic testing.