Journal

club
Pimlapas Leekitcharoenphon (Shinny)
Researcher
Research Group for Genomic Epidemiology
DTU Food
09-04-2019
Plan for today
9:00-9:45: Journal club

9:45-10:00: Results from mid-term report

10:00-10:15: Break

10:15-11:45: Other applicaMons of WGS

11.45-12.00: IntroducMon to poster exam
What was done:
²  A possible MRSA outbreak on a Special Care Baby Unit (SCBU)
was analyzed using convenMonal methods.

²  Colonized paMents from SCBU and MRSA isolates with the

same anMbioMc resistance profile from paMents in other wards
or from the community were whole-genome sequenced.
It all starts with 3 babies that at the same Mme
have an MRSA infecMon: P11, P12, and P13
Red: Resistant
White: SuscepMble
AnMbiogram profiles

Red: Resistant
White: SuscepMble
Epidemiological map of 14 infants from SCBU
New case a_er
cleaning?
A
Possible
outbreak?

Not the same

anMbioMcs
resistance
profile – not the
same outbreak

Then they start sequencing…

 PhylogeneMc tree based on “core” snps

•  Why “core” SNPs ?

•  Choice of reference ?
PhylogeneMc tree based on “core” snps

All ST2371

Only 20 SNPs differen6ated these 14 isolates

AnMbiogram profiles

Red: Resistant

Green: IniMally tested as
suscepMble, but re-tesMng
shows it is resistant

White: SuscepMble
Extended search

•  MRSA isolates with similar anMbioMc resistance profiles from

other wards are sequenced (retro- and prospecMvely) = 19
isolates
•  Ten of these are also ST2371
The other ST2371 isolates were all closely related to
the 14 infant-associated ST2371 isolates with 34 SNPs
The 10 new cases might be linked to SCBU through a previously undetected trainsmission
 Epidemiological map, incl. 10 cases outside the SCBU
New case P15
aKer 64 days
The re-emergence aKer the
deep clean led them suspect
that one or more member
of staff might be carrying
and transmiMng the OB
MRSA strain

154 employees are screened for MRSA

– ONE is found posiMve for ST2371
1 SNPs between P15 and P24
AnMbiogram profiles for the later cases
Epidemiological map, incl. 11 cases outside the
SCBU and one employee.
 Conclusion
•  WGS performed beeer for idenMfying paMents
and ciMzens part of the outbreak
•  IdenMficaMon of the outbreak led to an
invesMgaMon and the idenMficaMon of a
hospital employed carrier
 WGS advantages
•  High discriminatory power between closely
related bacterial isolates
•  Cost
–  Costs to the outbreak in the hospital was in excess
of £10,000
–  WGS of one MRSA isolate is £95 (in 2013)
•  Turnaround Mme
•  RouMne WGS -> database of WGS
 WGS advantages
•  ImplementaMon of rouMne WGS
–  Central database for comparison of sequence data
with previous local, naMonal and global isolates
–  Problem with sharing data
–  System for automated interpretaMon and linking
of genome sequence data