Real-Time Genome Sequencing of Resistant Bacteria Provides Precisio...

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Real-Time Genome Sequencing of
Resistant Bacteria Provides
Precision Infection Control in an
Institutional Setting
Dag Har...

Antibiotic Resistance: a Global Concern
“The problem is so serious that it threatens the achievements
of modern medicine. ...

Setting
MRSA, VRE, carbapenem-resistant Gram-
negative bacteria (4MDR-GN) are isolated on
every ward
carbapenem-susceptibl...

Real-time WGS of Multidrug Resistant
(MDR) Bacteria – an Interventional Study
• Study goals
– Interval I: Is prospective r...

Study Timeline
Documentation of
– turn-around time (TAT) from sample entry to completed
sequence (incl. potential repeated...

WGS Methods
• Overnight broth culture of pure culture
• DNA extraction: Qiagen MagAttract HMW Kit
• Library prep: Illumina...

Quality Control and Data nalysis
• Sequencing run QC
– cluster density and Q30 value above manufacturer´s
specifications
•...

Interval I:
Prospective Real-time WGS is Feasible
• In total 645 MDR bacteria sequenced
– 412 MRSA
– 102 MDR E. coli
– 79 ...

Interval I: Summary of Sequencing Results
& TAT (n = 645 MDR bacteria)
Organism
(total no.)
Mean % of
successfully
extract...

Interval I: WGS-based Typing of All MRSA
Exhibiting 71 Different spa Types
Epidemic curve of all 412 MRSA
(each box = sing...

Interval I: Diversity of LA-MRSA of
spa Type t011 (n=66)
Minimum-spanning tree
based on allelic profiles
based on 1,861 ta...

Interval I:
Cost Calculation for Sequencing
• Prerequisites
– 645 isolates, overall including all repeats 752 samples
sequ...

Interval I:
Costs for Sequencing
Organism (total no.)
€ / sample
(incl. VAT)
€ / isolate
(incl. 16.6% repeated
samples; in...

Interval I: Conclusions
• WGS on a routine basis is feasible
• Mean measured TAT of 4.4 to 5.3 days influence
decisions to...

Intervention and Interval II
• Change of infection control procedures (11 Jul 14)
– Stopping of preemptive isolation of pa...

Interval II:
Sequenced MDR Bacteria
• In total 598 isolates sequenced
– MRSA (n=325)
– E. coli (n=120)
– VRE (n=56)
– P. a...

Transmission Rates of MRSA and 3MDR-
GN E. coli During the Two Study Intervals
Study interval
Pathogen
(no. of isolates /
...

Cost-efficiency in Our Hospital Setting?
- Assumptions -
• Beds in multi-bed rooms are blocked if a patient is
positive fo...

WGS-based Surveillance is Cost-effective
• Interval I
– Overall sequencing costs: 130,608.84 €
– Costs for isolation calcu...

Laboratory Workflow Improvements
• Manual DNA extraction (Köser et al. 2013. JAC 69: 1275, PubMed)
and library preparation...

Bioinformatic Workflow Improvements
• SeqSphere+ pipelines automatically de novo
assembles the data and triggers cluster e...

Summary
• Transmissions are quite rare; exclusions of
transmissions are most common situations
• Rule-out majority of isol...

Acknowledgements
• Inst. Hygiene, Univ. Hosp. Münster, Germany
– U. Keckevoet, I. Höfig, T. Boeking, S. Bletz , A.
Mellman...

Real-Time Genome Sequencing of
Resistant Bacteria Provides
Precision Infection Control in an
Institutional Setting
Dag Har...

Interval I: Reasons for Sequencing Failures
Organism
(total no.)
Reasons for sequencing failure (no. of samples)
S. aureus...

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