B J Metcalf1, S Chochua1, R E Gertz1, P A Hawkins1, J Ricaldi1, Z Li1, H Walker1, T Tran1, J Rivers1, S Mathis1, D Jackson1, A Glennen2, R Lynfield2, L McGee1, B Beall3. 1. National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA. 2. Minnesota Department of Health, St Paul, MN, USA. 3. National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA. Electronic address: bbeall@cdc.gov.
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. Published by Elsevier Ltd.
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. Published by Elsevier Ltd.
Entities:
Keywords:
Accessory and core resistome; Antimicrobial susceptibility testing; Capsular serotyping; Group B streptococci; Whole genome sequence
Authors: James M Musser; Stephen B Beres; Luchang Zhu; Randall J Olsen; Jaana Vuopio; Hanne-Leena Hyyryläinen; Kirsi Gröndahl-Yli-Hannuksela; Karl G Kristinsson; Jessica Darenberg; Birgitta Henriques-Normark; Steen Hoffmann; Dominque A Caugant; Andrew J Smith; Diane S J Lindsay; David M Boragine; Timothy Palzkill Journal: J Clin Microbiol Date: 2020-03-25 Impact factor: 5.948
Authors: Srinivas Acharya Nanduri; Susan Petit; Chad Smelser; Mirasol Apostol; Nisha B Alden; Lee H Harrison; Ruth Lynfield; Paula S Vagnone; Kari Burzlaff; Nancy L Spina; Elizabeth M Dufort; William Schaffner; Ann R Thomas; Monica M Farley; Jennifer H Jain; Tracy Pondo; Lesley McGee; Bernard W Beall; Stephanie J Schrag Journal: JAMA Pediatr Date: 2019-03-01 Impact factor: 16.193
Authors: Gregory L Armstrong; Duncan R MacCannell; Jill Taylor; Heather A Carleton; Elizabeth B Neuhaus; Richard S Bradbury; James E Posey; Marta Gwinn Journal: N Engl J Med Date: 2019-12-26 Impact factor: 91.245
Authors: Kirsten S Vannice; Jessica Ricaldi; Srinivas Nanduri; Ferric C Fang; John B Lynch; Chloe Bryson-Cahn; Theodore Wright; Jeff Duchin; Meagan Kay; Sopio Chochua; Chris A Van Beneden; Bernard Beall Journal: Clin Infect Dis Date: 2020-06-24 Impact factor: 9.079
Authors: Lesley McGee; Sopio Chochua; Zhongya Li; Saundra Mathis; Joy Rivers; Benjamin Metcalf; Alison Ryan; Nisha Alden; Monica M Farley; Lee H Harrison; Paula Snippes Vagnone; Ruth Lynfield; Chad Smelser; Alison Muse; Ann R Thomas; Stephanie Schrag; Bernard W Beall Journal: Clin Infect Dis Date: 2021-03-15 Impact factor: 9.079