Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA. (August 2017)

• Record Type: Journal Article
• Authors: Reingold, A.; Brooks, S.; Randel, H.; Miller, L.; White, B.; Aragon, D.; Barnes, M.; Sadlowski, J.; Petit, S.; Cartter, M.; Marquez, C.; Wilson, M.; Farley, M.; Thomas, S.; Tunali, A.; Baughman, W.; Harrison, L.; Benton, J.; Carter, T.; Hollick, R.; Holmes, K.; Riner, A.; Holtzman, C.; Danila, R.; MacInnes, K.; Scherzinger, K.; Angeles, K.; Bareta, J.; Butler, L.; Khanlian, S.; Mansmann, R.; Nichols, M.; Bennett, N.; Zansky, S.; Currenti, S.; McGuire, S.; Thomas, A.; Schmidt, M.; Thompson, J.; Poissant, T.; Schaffner, W.; Barnes, B.; Leib, K.; Dyer, K.; McKnight, L.; Almendares, O.; Hudson, J.; McGlone, L.; Whitney, C.; Schrag, S.; Langley, G.; Metcalf, B.J.; Chochua, S.; Gertz, R.E.; Hawkins, P.A.; Ricaldi, J.; Li, Z.; Walker, H.; Tran, T.; Rivers, J.; Mathis, S.; Jackson, D.; Glennen, A.; Lynfield, R.; McGee, L.; Beall, B.;
• Is Part Of: Clinical microbiology and infection. Volume 23:Number 8(2017)
• Page Start: 574.e7
• Page End: 574.e14
• Publication Date: 2017-08
• Subjects: Accessory and core resistome -- Antimicrobial susceptibility testing -- Capsular serotyping -- Group B streptococci -- Whole genome sequence; Medical microbiology -- Periodicals; Diagnostic microbiology -- Periodicals; Communicable diseases -- Periodicals; Infection -- Periodicals; 616.01
• DOI: 10.1016/j.cmi.2017.02.021
• Languages: English
• ISSNs: 1198-743X

Abstract

Abstract: Objectives: Our 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). Methods: For 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. Results: All 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. Conclusion: The WGS-based assignment of iGBS resistance features and serotypes is an accurate substitute for phenotypic testing.