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

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.

Metcalf BJ1, Chochua S1, Gertz RE Jr1, Hawkins PA1, Ricaldi J1, Li Z1, Walker H1, Tran T1, Rivers J1, Mathis S1, Jackson D1, Glennen A2, Lynfield R2, McGee L1, Beall B3; Active Bacterial Core surveillance team.

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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.