Presentation given during Cost AMiCI meeting in Tallinn Nov 2017 by Siiri Kõljalg MD, PhD University of Tartu Tartu University Hospital

1. 22.01.2018
1
AMR: view from the hospital’s
laboratory
Usage of AMCs in health‐care
settings
Siiri Kõljalg MD, PhD
University of Tartu
Tartu University Hospital
Tallinn 17.11.2017
• Siiri Kõljalg MD, PhD
• Tartu University hospital
– Lab of clinical microbiology
• University of Tartu
– Institute of Biomedicine and
Translational Medicine
Department of Microbiology
Main research field
Antibacterial resistance (ESBL,
MRSA etc)
Hospital acquired infections
(C. difficile,
Acinetobacter etc)

2. 22.01.2018
2
AMR: view from the hospital’s
laboratory
Antimicrobial resistance (AMR)
• AMR occurs naturally over time, usually
through genetic changes.
• Misuse/overuse of antimicrobials, poor
infection prevention and control are
accelerating this process
• Global problem
• Higher medical costs, prolonged hospital
stays, increased mortality

3. 22.01.2018
3
Clinical microbiology
• The adaptation of microbiological techniques to the
study of the etiological agents of infectious disease
History
• mid‐1800s lab tests to detect tuberculosis, cholera, typhoid
and diphtheria
first hospital laboratories
(Guys Hospital, Johns Hopkins Hospital)
• AM susceptibility testing
Fleming
– 1924 ditch plate technique (antiseptics)
– 1929 broth dilution technique (→MIC)
Heatley
– 1940 disk diffusion test
Fleming 1928 penicillin
Clinical microbiology
• Focus change
19th century True pathogens
20th century Opportunistic pathogens

4. 22.01.2018
4
Infections caused by true pathogens
• Single causative agent
• Characteristic clinical findings
• Diagnosis based on clinical
findings
• Treatment based on clinical
diagnosis
• Laboratory – confirmation of
diagnosis, epidemiology
• Developed countries 
(prophylaxis)
• Ex. diphteria, tetanus, plague
etc
True pathogens are capable of causing
disease in healthy persons with normal
immune defenses
Opisthotonus in a patient suffering from
tetanus
Infections caused by opportunistic
pathogens
• Different causative agents
– Patient’s own microbes
– Hospital microbes etc
• Treatment directly
dependent on lab results
(ID, AMR testing)
• Developed countries 
• Ex. sepsis, hospital acquired
pneumonia etc
Opportunistic pathogen‐ cause disease when
the host's defenses are compromised or when
they grow in part of the body that is not
natural to them

5. 22.01.2018
5
The goal of the Lab of clinical microbiology
• Correct treatment of infectious diseases
– Identification of infectious agents
– AMR testing
• Outbreak prevention
– Early detection of infected patients and
microbial carriers
– Epidemiologic surveillance
the ongoing and systematic collection, analysis,
and interpretation of health data
The goal of AM susceptibility testing
• Predict the in vivo success or failure of
antibiotic therapy
• In vitro tests under standardized conditions
• Test results combined with clinical information
• Selection of the most appropriate antibiotic
for the patient

6. 22.01.2018
6
Interpretation of susceptibility test
results
• Interpretive criteria for MIC/zone diameter of all
relevant antibiotics for most bacterial genera
1. microbiologic data (comparison of MIC/zone sizes on
a large number of bacterial strains)
2. pharmacokinetic/pharmacodynamic data
3. clinical studies results
(comparisons of MIC/zone diameter
with microbiological eradication and
clinical efficacy)
reviewed and updated
European Committee on Antimicrobial Susceptibility Testing
Breakpoint tables for interpretation of MICs and zone diameters
Version 7.1, valid from 2017‐03‐10
Clinical breakpoints are for everyday use in the clinical laboratory to advise on patient therapy.

7. 22.01.2018
7
Laboratory of clinical microbiology
Culture based microbiology
• 1st day
Culture based microbiology
• 2nd day

8. 22.01.2018
8
Culture based microbiology
• 3rd day
Molecular microbiology
• Identification
• Resistance gene testing
– Methicillin R – mecA, mecC
– VRE – vanA, vanB
– ESBL (carbapenemases, AmpC)
• Rapid, sensitive, specific
• Higher cost, limitations
• Cannot replace phenotypic AMR testing

9. 22.01.2018
9
For good laboratory practice
• Verification – a one‐time process completed before a
test or instrument is used for patient testing. The
performance characteristics being verified can include
sensitivity, specificity, precision, accuracy, and
predictive value
• Validation – once an instrument or test system has
been verified, validation demonstrates that it
repeatedly continues to give the expected results as
performed over time and continues to meet the
manufacturer’s claims
covers the complete analytical process – preanalytical,
analytical and postanalytical
Guidelines and standards

10. 22.01.2018
10
Disk diffusion method
Medium Mueller‐Hinton agar (4 mm thickness. pH 7.2‐7.4)
AB disks Storage at ‐20ºC
Inoculum McFarland 0.5 (108 bacteria/ml)
Incubator Temperature 35ºC
Atmosphere Ambient air
Guidelines
Sample collection
Test result interpretation

11. 22.01.2018
11
Quality control
internal
Growth media control
• sterility
• quality
Quality control
internal
AMR testing
• Growth media
• AB disks/strips
with type strains

12. 22.01.2018
12
Quality control
internal
• Temperature control
• Atmosphere control
Quality control
external

13. 22.01.2018
13
• AMR testing in routine ID diagnostics is a
complex process
• Science based
• Standardized
Sucsessful ID management
Patient
Society

14. 22.01.2018
14
Usage of AMCs in health‐care
settings
Hospital environment
• A link between microbial surface
contamination and infection was first
identified in the 1960s and the role of surfaces
in cross‐contamination has now been well
documented
• The hospital environment has been identified
as an ideal ‘reservoir’ for micro‐organisms

15. 22.01.2018
15
Hospital environment
• The longer a nosocomial pathogen persists on
a surface, the longer it may be a source of
transmission and thus endanger a susceptible
patient or healthcare worker
• disinfectants lack of residual effect,
recontamination occurs quickly
Persistence of clinically relevant
bacteria on dry inanimate surfaces
Kramer et al. BMC Infect Dis. 2006
Type of microbe Duration of persistence (range)
Streptococcus pyogenes 3 days – 6.5 months
Staphylococcus aureus, incl MRSA 7 days – 7 months
Salmonella typhi 6 hours – 4 weeks
Escherichia coli 1.5 hours – 16 months
Clostridium difficile (spores) 5 months
Mycobacterium tuberculosis 1 day – 4 months
Candida albicans 1 – 4 months
Influenza virus 1 – 2 days

16. 22.01.2018
16
Common modes of transmission from inanimate
surfaces to susceptible patients
The options for antimicrobial surfaces
in hospitals
• Copper and silver have a natural antimicrobial feature
that delivers non‐stop bactericidal and fungicidal
protection to samples on contact.

17. 22.01.2018
17
Common modes of transmission from inanimate
surfaces to susceptible patients
AMC
AMC
 Antimicrobial surfaces (copper, silver, organosilane,
triclosan, QAC etc)
 AMC could help to reduce the rate of HAIs.
Antimicrobial surfaces in hospitals
• How do we test – and compare efficacy – of
antimicrobial surfaces?
• ISO 22916 – Antimicrobial products – Test for
antimicrobial activity and efficacy 2011
• Standardized tests have been proposed, but
not adopted widely Ojeil et al 2013; Agnihotri et al
2014
Intrinsic
resistance/tolerance

18. 22.01.2018
18
Acquired biocide resistance/tolerance
Acquired resistance/tolerance
Grey: sil‐positive isolates; white: sil‐negative isolates.
Swedish healthcare system ‐ restricted consumption of
silver‐based products
Risk group ‐ haematology and oncology patients
High frequency of silver resistance genes in invasive
isolates of Enterobacter and Klebsiella species
Sütterlin et al 2017 JHI
Phenotypical
resistance to
silver nitrate
13% Enterobacter
3% Klebsiella isolates.
single mutational event in
the silS gene
752 blood isolates

19. 22.01.2018
19
Acquired resistance/tolerance
Tolerance to quaternary ammonium compound disinfectants
may enhance growth of Listeria monocytogenes in the food
industry.
Møretrø et al 2017 JIFM
growth advantage at concentrations
of QAC present after sanitation
680 L. monocytogenes isolates
efflux genes qacH and bcrABC
increased tolerance to QAC
bcrABC ‐, qacH‐
bcrABC +, qacH+
0.001% of the benzalkonium chloride
based disinfectant DesQA.
2522 publicly available completely
sequenced bacterial genomes
565 different genera
Copper, silver, arsenic, antimony, cobalt, nickel, cadmium, iron, zinc, mercury and QACs
are all potential co‐selectors for strains resistant to, e.g.
sulfonamides, beta‐lactams, amphenicols, tetracyclines and aminoglycosides.
BMRG and ARG (horizontally transferrable)
Only ARGs
Only BMRG

20. 22.01.2018
20
The result of biocide resistance/tolerance
• Microbes survive
• Growth advantage
• Co‐resistance with AB
AB vs AMC
Antibiotics AMC
Administration/application Living Inanimate
topical environmental surfaces
oral invasive devices
i/v etc
Target Specific Non‐specific
Task Treatment Prevention
Prevention
Routine AMR testing Yes No
Standards Yes No
Resistance surveillance Yes No

21. 22.01.2018
21
AB vs AMC
Antibiotics AMC
Administration/application Living Inanimate
topical environmental surfaces
oral invasive devices
i/v etc
Target Specific Non‐specific
Task Treatment Prevention
Prevention
Routine AMR testing Yes No
Standards Yes No
Resistance surveillance Yes No
Conclusions
• Antibiotics are beneficial
• AMCs are beneficial
• To keep them beneficial in the future we need
– Research (basic & applied)
– Routine surveillance
– Dissemination of knowledge

22. 22.01.2018
22
Thank you!