Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

Claudio U. Koeser; Matthew Thomas Geoffrey Holden; Matthew J. Ellington; Edward J. P. Cartwright; Nicholas M. Brown; Amanda L. Ogilvy-Stuart; Li Yang Hsu; Claire Chewapreecha; Nicholas J. Croucher; Simon R. Harris; Mandy Sanders; Mark C. Enright; Gordon Dougan; Stephen D. Bentley; Julian Parkhill; Louise J. Fraser; Jason R. Betley; Ole B. Schulz-Trieglaff; Geoffrey P. Smith; Sharon J. Peacock

doi:10.1056/NEJMoa1109910

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

Claudio U. Koeser, Matthew Thomas Geoffrey Holden, Matthew J. Ellington, Edward J. P. Cartwright, Nicholas M. Brown, Amanda L. Ogilvy-Stuart, Li Yang Hsu, Claire Chewapreecha, Nicholas J. Croucher, Simon R. Harris, Mandy Sanders, Mark C. Enright, Gordon Dougan, Stephen D. Bentley, Julian Parkhill, Louise J. Fraser, Jason R. Betley, Ole B. Schulz-Trieglaff, Geoffrey P. Smith, Sharon J. Peacock^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

524 Citations (Scopus)

Abstract

BACKGROUND

Isolates of methicillin-resistant Staphylococcus aureus (MRSA) belonging to a single lineage are often indistinguishable by means of current typing techniques. Whole-genome sequencing may provide improved resolution to define transmission pathways and characterize outbreaks.

METHODS

We investigated a putative MRSA outbreak in a neonatal intensive care unit. By using rapid high-throughput sequencing technology with a clinically relevant turnaround time, we retrospectively sequenced the DNA from seven isolates associated with the outbreak and another seven MRSA isolates associated with carriage of MRSA or bacteremia in the same hospital.

RESULTS

We constructed a phylogenetic tree by comparing single-nucleotide polymorphisms (SNPs) in the core genome to a reference genome (an epidemic MRSA clone, EMRSA-15 [sequence type 22]). This revealed a distinct cluster of outbreak isolates and clear separation between these and the nonoutbreak isolates. A previously missed transmission event was detected between two patients with bacteremia who were not part of the outbreak. We created an artificial "resistome" of antibiotic-resistance genes and demonstrated concordance between it and the results of phenotypic susceptibility testing; we also created a "toxome" consisting of toxin genes. One outbreak isolate had a hypermutator phenotype with a higher number of SNPs than the other outbreak isolates, highlighting the difficulty of imposing a simple threshold for the number of SNPs between isolates to decide whether they are part of a recent transmission chain.

CONCLUSIONS

Whole-genome sequencing can provide clinically relevant data within a time frame that can influence patient care. The need for automated data interpretation and the provision of clinically meaningful reports represent hurdles to clinical implementation. (Funded by the U.K. Clinical Research Collaboration Translational Infection Research Initiative and others.)

Original language	English
Pages (from-to)	2267-2275
Number of pages	9
Journal	New England Journal of Medicine
Volume	366
Issue number	24
DOIs	https://doi.org/10.1056/NEJMoa1109910
Publication status	Published - 14 Jun 2012

Keywords

RESISTANT STAPHYLOCOCCUS-AUREUS
MUTATIONS
EVOLUTION

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10.1056/NEJMoa1109910

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Koeser, C. U., Holden, M. T. G., Ellington, M. J., Cartwright, E. J. P., Brown, N. M., Ogilvy-Stuart, A. L., Hsu, L. Y., Chewapreecha, C., Croucher, N. J., Harris, S. R., Sanders, M., Enright, M. C., Dougan, G., Bentley, S. D., Parkhill, J., Fraser, L. J., Betley, J. R., Schulz-Trieglaff, O. B., Smith, G. P., & Peacock, S. J. (2012). Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak. New England Journal of Medicine, 366(24), 2267-2275. https://doi.org/10.1056/NEJMoa1109910

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title = "Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak",

abstract = "BACKGROUNDIsolates of methicillin-resistant Staphylococcus aureus (MRSA) belonging to a single lineage are often indistinguishable by means of current typing techniques. Whole-genome sequencing may provide improved resolution to define transmission pathways and characterize outbreaks.METHODSWe investigated a putative MRSA outbreak in a neonatal intensive care unit. By using rapid high-throughput sequencing technology with a clinically relevant turnaround time, we retrospectively sequenced the DNA from seven isolates associated with the outbreak and another seven MRSA isolates associated with carriage of MRSA or bacteremia in the same hospital.RESULTSWe constructed a phylogenetic tree by comparing single-nucleotide polymorphisms (SNPs) in the core genome to a reference genome (an epidemic MRSA clone, EMRSA-15 [sequence type 22]). This revealed a distinct cluster of outbreak isolates and clear separation between these and the nonoutbreak isolates. A previously missed transmission event was detected between two patients with bacteremia who were not part of the outbreak. We created an artificial {"}resistome{"} of antibiotic-resistance genes and demonstrated concordance between it and the results of phenotypic susceptibility testing; we also created a {"}toxome{"} consisting of toxin genes. One outbreak isolate had a hypermutator phenotype with a higher number of SNPs than the other outbreak isolates, highlighting the difficulty of imposing a simple threshold for the number of SNPs between isolates to decide whether they are part of a recent transmission chain.CONCLUSIONSWhole-genome sequencing can provide clinically relevant data within a time frame that can influence patient care. The need for automated data interpretation and the provision of clinically meaningful reports represent hurdles to clinical implementation. (Funded by the U.K. Clinical Research Collaboration Translational Infection Research Initiative and others.)",

keywords = "RESISTANT STAPHYLOCOCCUS-AUREUS, MUTATIONS, EVOLUTION",

author = "Koeser, {Claudio U.} and Holden, {Matthew Thomas Geoffrey} and Ellington, {Matthew J.} and Cartwright, {Edward J. P.} and Brown, {Nicholas M.} and Ogilvy-Stuart, {Amanda L.} and Hsu, {Li Yang} and Claire Chewapreecha and Croucher, {Nicholas J.} and Harris, {Simon R.} and Mandy Sanders and Enright, {Mark C.} and Gordon Dougan and Bentley, {Stephen D.} and Julian Parkhill and Fraser, {Louise J.} and Betley, {Jason R.} and Schulz-Trieglaff, {Ole B.} and Smith, {Geoffrey P.} and Peacock, {Sharon J.}",

year = "2012",

month = jun,

day = "14",

doi = "10.1056/NEJMoa1109910",

language = "English",

volume = "366",

pages = "2267--2275",

journal = "New England Journal of Medicine",

issn = "0028-4793",

publisher = "Massachusetts Medical Society",

number = "24",

}

Koeser, CU, Holden, MTG, Ellington, MJ, Cartwright, EJP, Brown, NM, Ogilvy-Stuart, AL, Hsu, LY, Chewapreecha, C, Croucher, NJ, Harris, SR, Sanders, M, Enright, MC, Dougan, G, Bentley, SD, Parkhill, J, Fraser, LJ, Betley, JR, Schulz-Trieglaff, OB, Smith, GP & Peacock, SJ 2012, 'Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak', New England Journal of Medicine, vol. 366, no. 24, pp. 2267-2275. https://doi.org/10.1056/NEJMoa1109910

TY - JOUR

T1 - Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

AU - Koeser, Claudio U.

AU - Holden, Matthew Thomas Geoffrey

AU - Ellington, Matthew J.

AU - Cartwright, Edward J. P.

AU - Brown, Nicholas M.

AU - Ogilvy-Stuart, Amanda L.

AU - Hsu, Li Yang

AU - Chewapreecha, Claire

AU - Croucher, Nicholas J.

AU - Harris, Simon R.

AU - Sanders, Mandy

AU - Enright, Mark C.

AU - Dougan, Gordon

AU - Bentley, Stephen D.

AU - Parkhill, Julian

AU - Fraser, Louise J.

AU - Betley, Jason R.

AU - Schulz-Trieglaff, Ole B.

AU - Smith, Geoffrey P.

AU - Peacock, Sharon J.

PY - 2012/6/14

Y1 - 2012/6/14

N2 - BACKGROUNDIsolates of methicillin-resistant Staphylococcus aureus (MRSA) belonging to a single lineage are often indistinguishable by means of current typing techniques. Whole-genome sequencing may provide improved resolution to define transmission pathways and characterize outbreaks.METHODSWe investigated a putative MRSA outbreak in a neonatal intensive care unit. By using rapid high-throughput sequencing technology with a clinically relevant turnaround time, we retrospectively sequenced the DNA from seven isolates associated with the outbreak and another seven MRSA isolates associated with carriage of MRSA or bacteremia in the same hospital.RESULTSWe constructed a phylogenetic tree by comparing single-nucleotide polymorphisms (SNPs) in the core genome to a reference genome (an epidemic MRSA clone, EMRSA-15 [sequence type 22]). This revealed a distinct cluster of outbreak isolates and clear separation between these and the nonoutbreak isolates. A previously missed transmission event was detected between two patients with bacteremia who were not part of the outbreak. We created an artificial "resistome" of antibiotic-resistance genes and demonstrated concordance between it and the results of phenotypic susceptibility testing; we also created a "toxome" consisting of toxin genes. One outbreak isolate had a hypermutator phenotype with a higher number of SNPs than the other outbreak isolates, highlighting the difficulty of imposing a simple threshold for the number of SNPs between isolates to decide whether they are part of a recent transmission chain.CONCLUSIONSWhole-genome sequencing can provide clinically relevant data within a time frame that can influence patient care. The need for automated data interpretation and the provision of clinically meaningful reports represent hurdles to clinical implementation. (Funded by the U.K. Clinical Research Collaboration Translational Infection Research Initiative and others.)

AB - BACKGROUNDIsolates of methicillin-resistant Staphylococcus aureus (MRSA) belonging to a single lineage are often indistinguishable by means of current typing techniques. Whole-genome sequencing may provide improved resolution to define transmission pathways and characterize outbreaks.METHODSWe investigated a putative MRSA outbreak in a neonatal intensive care unit. By using rapid high-throughput sequencing technology with a clinically relevant turnaround time, we retrospectively sequenced the DNA from seven isolates associated with the outbreak and another seven MRSA isolates associated with carriage of MRSA or bacteremia in the same hospital.RESULTSWe constructed a phylogenetic tree by comparing single-nucleotide polymorphisms (SNPs) in the core genome to a reference genome (an epidemic MRSA clone, EMRSA-15 [sequence type 22]). This revealed a distinct cluster of outbreak isolates and clear separation between these and the nonoutbreak isolates. A previously missed transmission event was detected between two patients with bacteremia who were not part of the outbreak. We created an artificial "resistome" of antibiotic-resistance genes and demonstrated concordance between it and the results of phenotypic susceptibility testing; we also created a "toxome" consisting of toxin genes. One outbreak isolate had a hypermutator phenotype with a higher number of SNPs than the other outbreak isolates, highlighting the difficulty of imposing a simple threshold for the number of SNPs between isolates to decide whether they are part of a recent transmission chain.CONCLUSIONSWhole-genome sequencing can provide clinically relevant data within a time frame that can influence patient care. The need for automated data interpretation and the provision of clinically meaningful reports represent hurdles to clinical implementation. (Funded by the U.K. Clinical Research Collaboration Translational Infection Research Initiative and others.)

KW - RESISTANT STAPHYLOCOCCUS-AUREUS

KW - MUTATIONS

KW - EVOLUTION

U2 - 10.1056/NEJMoa1109910

DO - 10.1056/NEJMoa1109910

M3 - Article

SN - 0028-4793

VL - 366

SP - 2267

EP - 2275

JO - New England Journal of Medicine

JF - New England Journal of Medicine

IS - 24

ER -

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

Abstract

Keywords

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