200. Whole-Genome Sequencing of Multidrug-Resistant (MDR) Escherichia coli Isolates from Community Hospitals in North Carolina, 2010-2015
Session: Poster Abstract Session: Diagnostics: Bacteriology, Sequencing, and Resistance
Thursday, October 27, 2016
Room: Poster Hall
  • 20161013ESBL-WGS_poster_IDWeek2016final.pdf (1.4 MB)
  • Background: Escherichia coli sequence type 131 (ST131), associated with CTX-M-15-type ESBLs, currently predominates among MDR E. coli in both healthcare and community settings in the United States and worldwide. Here, we used whole-genome sequencing (WGS) to investigate MDR E. coli from community hospitals.

    Methods: Sixty-three non-duplicate clinical isolates of MDR E. coli collected from 6 North Carolina community hospitals (2010-2015) were analyzed. Size-fractionated DNA libraries were labeled, pooled, and sequenced in an Illumina HiSeq2500 run. Multi-locus sequence typing (MLST) and detection of acquired resistance genes and plasmids were done using a bioinformatic pipeline available at the Center for Genomic Epidemiology. Reads were aligned against EC958, and pairwise single-nucleotide variant (SNV) differences between isolates were calculated. Within ST131, subclones H30R (fimH allele 30; ciprofloxacin-resistant) and H30Rx (a CTX-M-15-associated H30R subset; defined by SNV G723A in ybbW) were identified as described previously. A maximum-likelihood phylogram and recombination map were constructed using Gubbins.

    Results: Of the 63 study isolates, in silico MLST identified 39 (62%) as ST131, of which 35 (90%) were H30R and 25 (64%) were H30Rx. Of the remaining 24 (38% of 63) non-ST131 isolates, 6 (25%) were ST405. The ST131 strains contained CTX-M-15 (N=27, 69%), CTX-M-14 (N=4, 10%), and CTX-M-27 (N=1), but not SHV or TEM. Whereas CTX-M-15 was closely associated with H30Rx, other CTX-M types were associated with non-Rx H30 or non-ST131 strains (Fig. 1). IncFIA was present in 34 ST131 strains (87%), IncFIB in 16 (41%), and IncFII in 35 (90%), and segregated by ST131 subclone (Fig. 1). In pairwise comparisons, the various ST131 core genomes differed by 0-11,939 SNVs overall, vs. by 0-733 SNVs within H30R or H30Rx. The phylogeny demonstrated differentiation of MDR E. coli strains and development of clades (Fig. 2 and 3). No temporal clustering was evident.

    Conclusion: WGS analysis of our community hospital MDR E. coli isolates suggested ongoing circulation of E. coli ST131, with clonal segregation of CTX-M variants, other resistance genes, and Inc-type plasmids. The high prevalence of CTX-M-15 was driven mainly by the H30Rx subclone.

    Hajime Kanamori, MD, PhD, MPH1, Christian Parobek, PhD2, Jonathan Juliano, MD, MSPH1, James R. Johnson, MD, FIDSA, FACP, FRCPE3, Brian D. Johnston, BA4, David J. Weber, MD, MPH, FIDSA, FSHEA5, William Rutala, PhD, MPH, FSHEA6 and Deverick Anderson, MD, MPH, FIDSA, FSHEA7, (1)Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, (2)University of North Carolina School of Medicine, Chapel Hill, NC, (3)Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, MN, (4)Minneapolis Veterans Affairs Health Care System, Minneapolis, MN, (5)Medicine, Pediatrics, Epidemiology, University of North Carolina, School of Public Health, Chapel Hill, NC, (6)Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill, NC, (7)Division of Infectious Diseases, Duke University Medical Center, Durham, NC


    H. Kanamori, None

    C. Parobek, None

    J. Juliano, None

    J. R. Johnson, None

    B. D. Johnston, None

    D. J. Weber, None

    W. Rutala, None

    D. Anderson, None

    Findings in the abstracts are embargoed until 12:01 a.m. CDT, Wednesday Oct. 26th with the exception of research findings presented at the IDWeek press conferences.