Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.
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.).
University of Cambridge, Cambridge, United Kingdom.
Claudio U
CU
Köser
Matthew T G
MT
Holden
Matthew J
MJ
Ellington
Edward J P
EJ
Cartwright
Nicholas M
NM
Brown
Amanda L
AL
Ogilvy-Stuart
Li Yang
LY
Hsu
Claire
C
Chewapreecha
Nicholas J
NJ
Croucher
Simon R
SR
Harris
Mandy
M
Sanders
Mark C
MC
Enright
Gordon
G
Dougan
Stephen D
SD
Bentley
Julian
J
Parkhill
Louise J
LJ
Fraser
Jason R
JR
Betley
Ole B
OB
Schulz-Trieglaff
Geoffrey P
GP
Smith
Sharon J
SJ
Peacock
D016470:Bacteremia / Q000453:epidemiology / Q000382:microbiology*; D003428:Cross Infection / Q000453:epidemiology / Q000382:microbiology; D004269:DNA, Bacterial / Q000032:analysis; D004196:Disease Outbreaks; D016680:Genome, Bacterial; D006801:Humans; D007231:Infant, Newborn; D007363:Intensive Care Units, Neonatal; D016106:Methicillin Resistance / Q000235:genetics; D055624:Methicillin-Resistant Staphylococcus aureus / Q000235:genetics* / Q000302:isolation & purification; D008826:Microbial Sensitivity Tests; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA / Q000379:methods; D013203:Staphylococcal Infections / Q000453:epidemiology* / Q000382:microbiology
D004269:DNA, Bacterial