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Case Reports
. 2019 Feb 13:11:3.
doi: 10.1186/s13099-019-0288-7. eCollection 2019.

High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei

Leigh G Monahan  1 , Matthew Z DeMaere  1 , Max L Cummins  1 , Steven P Djordjevic  1 , Piklu Roy Chowdhury  1   2 , Aaron E Darling  1
Affiliations
Case Reports

High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei

Leigh G Monahan et al. Gut Pathog. .

Abstract

Background: Enterobacter hormaechei is an important emerging pathogen and a key member of the highly diverse Enterobacter cloacae complex. E. hormaechei strains can persist and spread in nosocomial environments, and often exhibit resistance to multiple clinically important antibiotics. However, the genomic regions that harbour resistance determinants are typically highly repetitive and impossible to resolve with standard short-read sequencing technologies.

Results: Here we used both short- and long-read methods to sequence the genome of a multidrug-resistant hospital isolate (C15117), which we identified as E. hormaechei. Hybrid assembly generated a complete circular chromosome of 4,739,272 bp and a fully resolved plasmid of 339,920 bp containing several antibiotic resistance genes. The strain also harboured a 34,857 bp repeat encoding copper resistance, which was present in both the chromosome and plasmid. Long reads that unambiguously spanned this repeat were required to resolve the chromosome and plasmid into separate replicons.

Conclusion: This study provides important insights into the evolution and potential spread of antimicrobial resistance in a nosocomial E. hormaechei strain. More broadly, it further exemplifies the power of long-read sequencing technologies, particularly the Oxford Nanopore platform, for the characterisation of bacteria with complex resistance loci and large repeat elements.

Keywords: Enterobacter cloacae complex; Enterobacter hormaechei; Hybrid assembly; Long-read sequencing.

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Figures

Fig. 1
Fig. 1
Phylogenetic analysis identifies C15117 as most closely related to Enterobacter hormaechei susbp. oharae. Representative strains from 18 ECC phylogenomic groups (labelled A to R in square brackets) were included in the analysis. Bootstrap support values are shown at the nodes of the tree. Branch length has been normalised to substitutions per site
Fig. 2
Fig. 2
Distribution of read lengths generated on the PacBio RSII (top) and the ONT MinION (bottom) for E. hormaechei C15117. Maximum read lengths were 202,611 bp for ONT and 44,753 bp for PacBio; minima were 193 bp (ONT) and 35 bp (PacBio); means were 15,888 bp (ONT) and 11,881 bp (PacBio), while median lengths were 8462 bp (ONT) and 10,629 bp (PacBio)
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