Tel: +61 (0) 7 3346 6081Running title: Genomic investigation of an OXA-181 E. coli outbreak
Abstract:Background: OXA-48-like carbapenemases have become increasingly prevalent in healthcare settings worldwide. Their low-level activity against carbapenems makes them difficult to identify, causing problems for infection control. Here we present an outbreak of Escherichia coli producing OXA-181 (part of the OXA-48 family of carbapenemases) in a Queensland Hospital, and describe how we used whole genome sequencing (WGS) to identify the outbreak strain, determine the extent of transmission within the hospital and support infection control responses.Methods: 116 isolates were collected and sequenced on an Illumina NextSeq to determine species, sequence type (ST) and presence of resistance genes. Core single nucleotide polymorphisms were used to determine strain relatedness. Three isolates were also sequenced on an Oxford Nanopore MinION to determine the context of the resistance genes.
Results: Of 116 isolates, 85 (84 E. coli and one K. pneumoniae) from 78 patients (and two environmental sources) were related to the ongoing outbreak. The outbreak E. coli strain was found to be ST38 and carried blaOXA-181, blaCTX-M-15 and qnrS1 genes. Long read sequencing revealed blaOXA-181 to be carried on an IncX3 plasmid with qnrS1. blaCTX-M-15 was chromosomally integrated (via ISEcp1 insertion) in close proximity to a second qnrS1 gene. A search of the laboratory database identified an isolate with an identical unusual antibiogram from a patient recently admitted to a hospital in Vietnam, suggesting that the strain was introduced to the hospital. This De novo assembly: Illumina reads were de novo assembled using Spades v3.11.1 [16] under default settings. Filtered Nanopore reads were de novo assembled using Canu v1.7 [17] at default settings. Genotyping and gene detection methods: De novo assemblies for all isolates were screened for sequence type (ST) using the tool mlst v2.1 [18] which incorporates components of the PubMLST database [19]. The same assemblies were also screen for plasmid incompatibility (Inc) types, resistance genes and virulence genes using Abricate v0.8 [20]. Plasmidfinder [21], VFDB [22] and a non-redundant Resfinder [23] + ARG-ANNOT [24] database (last updated April 2018). The Illumina de novo assemblies were used to determine the following: [i] O and H types by screening the EcOH database (updated 18 January 2019) using Abricate [20]; [ii] K type using Kaptive (v0.5.1) [25] against an in-house E. coli capsule database; and [iii] fimH antigen using Fimtyper (v1.1) [26]. The de novo assembly of SS17M6399 and the complete reference genome MS14441was analysed using the web-based tool PHASTER [27] (accessed 20/5/2019). SNP distance and relationship matrix: Illumina reads were mapped to the concatenated de novo short-read assembly for MS14445 using Bowtie v2.3.4.2 [28](as implemented in Nesoni [14]). Core single nucleotide polymorphisms (SNPs) and single nucleotide indels were called using Nesoni from a core genome ...