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

Active Bacterial Core surveillance team

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)574.e7-574.e14
JournalClinical Microbiology and Infection
Volume23
Issue number8
DOIs
StatePublished - Aug 1 2017

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Streptococcus agalactiae
Genome
Lincosamides
Lactams
Erythromycin
Streptogramin A
Genes
Serotyping
Trimethoprim
Clindamycin
Fluoroquinolones
Macrolides
Chloramphenicol
Vancomycin
Rifampin
Centers for Disease Control and Prevention (U.S.)
Tetracycline
Computational Biology
rRNA Genes
Serogroup

Keywords

  • Accessory and core resistome
  • Antimicrobial susceptibility testing
  • Capsular serotyping
  • Group B streptococci
  • Whole genome sequence

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

Cite this

Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA. / Active Bacterial Core surveillance team.

In: Clinical Microbiology and Infection, Vol. 23, No. 8, 01.08.2017, p. 574.e7-574.e14.

Research output: Contribution to journalArticle

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title = "Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA",
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.",
keywords = "Accessory and core resistome, Antimicrobial susceptibility testing, Capsular serotyping, Group B streptococci, Whole genome sequence",
author = "{Active Bacterial Core surveillance team} and Metcalf, {B. J.} and S. Chochua and Gertz, {R. E.} and Hawkins, {P. A.} and J. Ricaldi and Z. Li and H. Walker and T. Tran and J. Rivers and S. Mathis and D. Jackson and L. McGee and B. Beall and A. Glennen and R. Lynfield and A. Reingold and S. Brooks and H. Randel and L. Miller and B. White and D. Aragon and M. Barnes and J. Sadlowski and S. Petit and M. Cartter and C. Marquez and M. Wilson and M. Farley and S. Thomas and A. Tunali and W. Baughman and L. Harrison and J. Benton and T. Carter and Hollick, {Rosemary A} and K. Holmes and A. Riner and C. Holtzman and R. Danila and K. MacInnes and K. Scherzinger and K. Angeles and J. Bareta and L. Butler and S. Khanlian and R. Mansmann and M. Nichols and N. Bennett and S. Zansky and S. Currenti",
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TY - JOUR

T1 - Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA

AU - Active Bacterial Core surveillance team

AU - Metcalf, B. J.

AU - Chochua, S.

AU - Gertz, R. E.

AU - Hawkins, P. A.

AU - Ricaldi, J.

AU - Li, Z.

AU - Walker, H.

AU - Tran, T.

AU - Rivers, J.

AU - Mathis, S.

AU - Jackson, D.

AU - McGee, L.

AU - Beall, B.

AU - Glennen, A.

AU - Lynfield, R.

AU - Reingold, A.

AU - Brooks, S.

AU - Randel, H.

AU - Miller, L.

AU - White, B.

AU - Aragon, D.

AU - Barnes, M.

AU - Sadlowski, J.

AU - Petit, S.

AU - Cartter, M.

AU - Marquez, C.

AU - Wilson, M.

AU - Farley, M.

AU - Thomas, S.

AU - Tunali, A.

AU - Baughman, W.

AU - Harrison, L.

AU - Benton, J.

AU - Carter, T.

AU - Hollick, Rosemary A

AU - Holmes, K.

AU - Riner, A.

AU - Holtzman, C.

AU - Danila, R.

AU - MacInnes, K.

AU - Scherzinger, K.

AU - Angeles, K.

AU - Bareta, J.

AU - Butler, L.

AU - Khanlian, S.

AU - Mansmann, R.

AU - Nichols, M.

AU - Bennett, N.

AU - Zansky, S.

AU - Currenti, S.

PY - 2017/8/1

Y1 - 2017/8/1

N2 - 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.

AB - 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.

KW - Accessory and core resistome

KW - Antimicrobial susceptibility testing

KW - Capsular serotyping

KW - Group B streptococci

KW - Whole genome sequence

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