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FT-IR spectroscopy: an effective method for

real-time outbreak investigation

Jonathan Lellouche, Ph.D

National Laboratory for Antibiotic Resistance andInvestigation of Outbreaks in Medical Institutions

Ministry of Health, State of Israel

September 18, 2019© ESCMID

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What is the ideal bacterial typing method?

The laboratory side…

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Easy to perform

Fast results/short turnaround time

User friendly

Low costs in reagents

Applicable for all types of bacteria

Doesn’t require highly specialized facilities (e.g. PCR labs)

Reduced post-analytical analyses (e.g WGS)

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We need to provide an effective tool to:

• Understand the epidemiology of the outbreak

• Support investigation and focus teams to appropriate intervention

• Monitoring the outbreak trends

• To improve infection control program and hygiene management

Typing method role in an outbreak event

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Case No. 1 + Case No. 2 + Case No. X…

Suspected outbreak

Primary report

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Investigation4

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Preliminary results

Intervention

6 Final results

7 Active surveillance

Comparison to data from the past

Schematic overview of a typical outbreak

Fast results, easiness of use

Reproducibility, robustness, discriminatory power

Cost and resources

Time

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IR Biotyper

• Received at the National Laboratory for Antibiotic Resistance at the end

of 2018

• Utilized in more than 20 outbreaks

• The system was validated for several bacteria

- E. cloacae

- P. aeruginosa

- A. baumannii

- K. pneumoniae

- S. aureus

- E. faecium /faecalis

• Active surveillance (on-going validation)

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Case No.1: S. marcescens bloodstream infections outbreak

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Background

In March 2019, the MOH received notification of five patients from a single outpatient

hemodialysis clinic who had presented to a nearby general hospital with S. marcescensbacteremia within a period of two weeks.

IR Biotyper Rep-PCR

• Preliminary results were obtained within few hours after samples receiving

• IC staff began the intervention with the confirmation of monoclonal outbreak

• Secondary results excluded environmental source contamination

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Case No.2: VIM-producing E. cloacae outbreak

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2017-outbreak

2019-outbreak

Background

• In August 2019, the Israel MOH received notification of five patients from a general

hospital with different clinical outcomes including bacteremia.

• VIM-producing E. cloacae was isolated from clinical samples

• A major cluster composed by 3 patients and 2 satellites were identified

• We excluded a relationship with a VIM-producing E. cloacae monoclonal outbreak

from 2017 involving ~30 patients in the same hospital.© ESCMID

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Case No. 3: IMI-producing E. cloacae outbreak

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Background

• June 2019: report with IMI-positive rectal swabs in 5 patients (without clinical

outcomes) in the same day from a general hospital from the center of Israel.

• Under a short period of two weeks, 25 additional carriers were identified. A

total of 42 patients were recorded.

• Investigation was performed, IC measures were taken but the source of

contamination was not identified

The prevalence of blaIMI is low, between 2014-2018 less than 30 IMI-producing E.

cloacae cases were reported in Israel

All IMI-positive isolates were typed as an active surveillance action© ESCMID eL

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2019: pIMI-6

2014-2018 IMI-2 isolates

2019: unexplained IMI-6 satellites

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6 isolates from 3 different hospital were received and confirmed as the same clone

by WGS and core genome alignment

Changes in guidelines were envisaged regarding the blaIMI gene detection

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Case No 4: long-term MRSA outbreak

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Background

As a part of a program for the eradication of endemic MRSA in a rehabilitation center,

a screening for MRSA carriers was performed.

t911, pvl negative, qacA/B negative

t934

pvl positive

qacA/B positive

t008

t002

A complete agreement with spa typing were observed

IC control measures and cohorting efficacy improved

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Case No 5: VRE outbreakBackground

Investigation for vanA-E. faecium carriers in two internal department in a general

hospital.

Biotyper BOX

1 I A

2 III B

3 I A

4 II A

5 II C

6 II D

7 I A

8 II E

9 I A

10 I F

11 I A

12 I A

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Department No. 1

Department No. 2

One specific clone for each department was identified

Few discrepancies were recorded when compared to BOX-PCR analysis© ESCMID

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Case No. 6: CRAB outbreak

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OXA-71 high virulent strain

OXA-66

Capsulated CRAB sub-population

Background

Investigation for CRAB carriage in a long-term after two cases of high virulent

septicemia

Perfect agreement with OXA-51 typing method

FT-IR biotyping have a potential to identify sub-population based capsule presence

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Lab Team

David Schwartz

Sammy Frenk

Nadya Rakovitsky

Polet Elmalich

Hadas Kon

Reut Rov

Gabrielle Levi

Shirin Abramov

Amichay Hameir

National institute for Antibiotic resistance and Infection Control

Yehuda Carmeli

Mitchell Schwaber

Staff of the National Intitute for Infection Control

Ministry of Health – financial support

Technical support

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