Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia

Theodore R Pak; Deena R Altman; Oliver Attie; Robert Sebra; Camille L Hamula; Martha Lewis; Gintaras Deikus; Leah C Newman; Gang Fang; Jonathan Hand; Gopi Patel; Fran Wallach; Eric E Schadt; Shirish Huprikar; Harm van Bakel; Andrew Kasarskis; Ali Bashir

doi:10.1128/AAC.01723-15

Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia

Antimicrob Agents Chemother. 2015 Nov;59(11):7117-20. doi: 10.1128/AAC.01723-15. Epub 2015 Aug 31.

Authors

Theodore R Pak¹, Deena R Altman², Oliver Attie¹, Robert Sebra¹, Camille L Hamula³, Martha Lewis¹, Gintaras Deikus¹, Leah C Newman¹, Gang Fang¹, Jonathan Hand², Gopi Patel², Fran Wallach², Eric E Schadt¹, Shirish Huprikar², Harm van Bakel¹, Andrew Kasarskis⁴, Ali Bashir¹

Affiliations

¹ Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
² Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
³ Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
⁴ Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA andrew.kasarskis@mssm.edu.

Abstract

Whole-genome sequences for Stenotrophomonas maltophilia serial isolates from a bacteremic patient before and after development of levofloxacin resistance were assembled de novo and differed by one single-nucleotide variant in smeT, a repressor for multidrug efflux operon smeDEF. Along with sequenced isolates from five contemporaneous cases, they displayed considerable diversity compared against all published complete genomes. Whole-genome sequencing and complete assembly can conclusively identify resistance mechanisms emerging in S. maltophilia strains during clinical therapy.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

DNA, Bacterial / genetics
Drug Resistance, Multiple, Bacterial / genetics
Genome, Bacterial / genetics*
Gram-Negative Bacterial Infections / microbiology*
Microbial Sensitivity Tests
Mutation
Quinolones / pharmacology*
Stenotrophomonas maltophilia / immunology*

Substances

DNA, Bacterial
Quinolones

Supplementary concepts

Stenotrophomonas maltophilia bacteremia

Associated data