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.
J. Juliano, None
J. R. Johnson, None
B. D. Johnston, None
D. J. Weber, None
W. Rutala, None
D. Anderson, None
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