lunes, 13 de marzo de 2017

Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcu... - PubMed - NCBI

Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcu... - PubMed - NCBI



 2017 Feb 28. pii: S1198-743X(17)30118-0. doi: 10.1016/j.cmi.2017.02.021. [Epub ahead of print]

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

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 to 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 harbored 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 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 nonsusceptibility 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 (8 isolates), trimethoprim, chloramphenicol and vancomycin (2 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 thirty-two of 1975 isolates (1.6%), WGS-based serotypes could not be assigned.

CONCLUSION:

WGS-based assignment of iGBS resistance features and serotypes is an accurate substitute for phenotypic testing.

KEYWORDS:

Group B streptococci; accessory and core resistome; antimicrobial susceptibility testing; capsular serotyping; whole genome sequence

PMID:
 
28257899
 
DOI:
 
10.1016/j.cmi.2017.02.021
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