Intensive infection control responses and whole genome sequencing to interrupt and resolve widespread transmission of OXA-181 Escherichia coli in a hospital setting

Roberts, L. W.; Forde, B. M.; Henderson, A.; Playford, G.; Runnegar, N.; Henderson, B.; Watson, C.; Lindsay, M.; Bursle, E.; Douglas, J.; Paterson, D. L.; Schembri, M. A. A.; Harris, P. N. A.; Beatson, S. A.

doi:10.1101/850628

bioRxiv · 10.1101/850628

Intensive infection control responses and whole genome sequencing to interrupt and resolve widespread transmission of OXA-181 Escherichia coli in a hospital setting

Roberts, L. W.·Forde, B. M.·Henderson, A.·Playford, G.·Runnegar, N.·Henderson, B.·Watson, C.·Lindsay, M.·Bursle, E.·Douglas, J.·Paterson, D. L.·Schembri, M. A. A.·Harris, P. N. A.·Beatson, S. A.

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Abstract

BackgroundOXA-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. Methods116 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. ResultsOf 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 conclusion was supported by WGS, as comparison of the strain to public data identified a close match to an E. coli recovered from Vietnam in 2011. ConclusionA blaOXA-181-carrying E. coli ST38 strain was introduced to a Brisbane hospital and spread undetected throughout multiple wards over several months. Using WGS, we characterized the outbreak strain and unambiguously detected its presence throughout the hospital. We show how both WGS and infection control measures can be utilized to effectively terminate widespread transmission of an elusory pathogen.

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Roberts, L. W., Forde, B. M., Henderson, A., Playford, G., Runnegar, N., Henderson, B., Watson, C., Lindsay, M., Bursle, E., Douglas, J., Paterson, D. L., Schembri, M. A. A., Harris, P. N. A., Beatson, S. A.. 2019-11-30. Intensive infection control responses and whole genome sequencing to interrupt and resolve widespread transmission of OXA-181 Escherichia coli in a hospital setting. https://doi.org/10.1101/850628

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