microbial diagnostics - university of calgary in alberta

Ian Lewis, PhD; Assistant ProfessorAI Translational Health Chair

University of Calgary

www.lewisresearchgroup.org

Microbial diagnostics

AMR Course | Calgary, AB | 2020

Lewis Research Group

http://www.lewisresearchgroup.org/

Antibiotic resistance in Calgary

Drug sensitive

Drug Resistant

Ex1: BSI Test Ex2: UTI TestWhy omics? PIM Innovation

June 19th

18:15

June 24st

10:01

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Youtube video on microbiology testing

Emerging platforms for fast ID/AST


Direct MALDI-TOF mass spectrometry



Biofire film array (BCID panel) (Multiplex real-time PCR)



216DX UTI System (Laser light scattering)



T2 Candida Panel (T2 Magnetic Resonance)



Reveal AST (Volatile organic compound detection)



AStar (microscopy)



Phoenix Automated Microbiology System (Redox and Turbidity)

Kumar A et al. Crit Care Med 2006; 34:1589-96.

Deaths resulting from slow diagnostics


Can metabolism be used as a diagnostic platform?


Calgary Metabolomics Research Facility (CMRF)


Thomas Rydzak, PhDUniversity of Calgary

Metabolic Preference Assay

Apex/DynaLIFE NDA


Can microbes be identified via metabolism?

YesN = 23,000


Can antibiotic susceptibility can be measured by metabolism?


Yes, metabolite profiles are highly diagnostic

Can antibiotic susceptibility can be measured by metabolism?


Does it work? A blinded trial of Alberta

1. Every blood culture in Calgary

2. 10 days of collection

3. N = 775


https://albertaprecisionexchange.ca/

Sensitivity (%) Specificity (%)

Culture growth 96.1 99.8

Genus ID 84 87

n=775Species ID of 7 target species = 85.8%

Did it work? Yes!!!

negative

positive

Samples containing organisms not within training set Samples containing organisms within training set


The BIG Race


Tom wins!!!!!!


Why UTIs are a problem

• Most common form of bacterial infection

• Estimated cost of $2.6B USD annually

• Potentially life-threatening consequences

• Lifetime occurrence of 50-70% in women

Dan Gregson, MDCalgary Laboratory Services

Long diagnostic timelines: a familiar problem

Can metabolomics detect UTIs?


METHOD DEVELOPMENTMETHOD

1. Urine collected 2. 13C labeled standard added.

3. Target metabolites are isolated

4. LC-MS SRM analysis (<1min per sample)

Rapid screening assay for urinary tract infection



Spencer WildmanUniversity of Calgary


Tom versus Alberta Public Laboratories


Microbiome

Lukas F. Mager et al. Science, 2020

Yonatan GradHarvard School of Public Health

George ChaconasUniversity of Calgary

Kathy McCoyUniversity of Calgary

Steven NorrisUniversity of

Texas

Ex1: BSI Test Ex2: UTI TestWhy Omics? PIM Innovation

Rapid Infection Diagnostics Inc.

HOPPER – BSIDXTM and UTIDXTM test

Transwell with

engineered medium

and ABs

Vanquish sample hotel and

UHPLC

TSQ Altis Triple Quad ID database

What is APEX?Why APEX? APEX’s PotentialExample Project Achievements InnovationAchievementsEx1: BSI Test Ex2: UTI TestWhy Omics? PIM

Rapid diagnostics for automatable surveillance

What is APEX?Why APEX? APEX’s PotentialExample Project Achievements InnovationAchievementsEx1: BSI Test Ex2: UTI TestWhy Omics? PIM

AMR Surveillance

Simon Otto, PhD DVM BSc

Assistant Professor

[email protected]

We acknowledge and pay tribute to the traditional territories of the peoples of Treaty 6, which includes the Cree, Blackfoot, Métis, Nakota Sioux, Iroquois, Dene, Ojibway, Saulteaux, Anishinaabe, Inuit, and many others

whose histories, languages, and cultures continue to influence our vibrant community.

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mailto:[email protected]

Outline

1. Intro: Dr. Ian Lewis and Dr. Simon Otto

2. Integrated AMR/AMU surveillance

3. Dr. Lewis: AMR measurement and related

sections

4. Whole Genome Sequencing (WGS) for

AMR surveillance

5. Select AMR/AMU Surveillance Examples

6. Discussion

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Links to Course Learning

Outcomes

• Course Learning Outcomes:1. Complex contributing factors to AMU and the

emergence and spread of AMR.

3. The global interdependence of people, animals,

and the environment (One Health)

4. The role of One Health in complex problems

and AMR.

5. AMR surveillance requirements and mitigation

efforts.

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Learning Objectives (Simon)

• Objective 1: Explain the components of an integrated,

One Health surveillance system for AMR and AMU.

• Objective 2: Describe the opportunities and challenges

of using Whole Genome Sequencing for AMR

surveillance.

• Objective 3: Explain key examples of the application of

integrated, One Health AMR/AMU surveillance.

• Objective 4: Assess the gaps in One Health AMR/AMU

surveillance.

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Be thinking about…

• What does integration in an AMR/AMU

surveillance system entail?

– What must be integrated?

– Why is integration important to inform

stakeholders?

• Practitioners

• Industry

• Government and other policy makers

• Etc.

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Resources• Required resource:

– Miazga-Rodriguez M, Saxinger LM, Otto SJG. “How are we

doing? Progress on Integrated AMR and AMU Surveillance in

Canada: 2014-2019.”

• CPHA Public Health 2020 virtual abstract: https://youtu.be/PD7wGeA8hKU

• Supplemental reading:

– WHO AGISAR 2017 “Integrated surveillance of AMR in

foodborne bacteria Application of a One Health approach”

• https://www.who.int/foodsafety/publications/agisar_guidance2017/en/

– WHO 2020 “Global Antimicrobial Surveillance System - Whole-

genome sequencing for surveillance of AMR”

• https://www.who.int/publications/i/item/9789240011007

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https://youtu.be/PD7wGeA8hKU

https://www.who.int/foodsafety/publications/agisar_guidance2017/en/

https://www.who.int/publications/i/item/9789240011007

8http://www.phac-aspc.gc.ca/cipars-picra/gfx/epi-lg-eng.png

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http://www.phac-aspc.gc.ca/cipars-picra/gfx/epi-lg-eng.png

What is Surveillance?

• What is surveillance?

– “Information for Action” – Larry Svenson, AH

• What is monitoring?

– Surveillance without an action/response component

• “Systematic ongoing collection, collation, and analysis of

data and the timely dissemination of information to those

who need to know so that action can be taken.” - WHO

Purpose of AMR Surveillance

• AMR surveillance – “characterization AMR

pathogens and their distribution in the

population” – WHO 2020 GLASS WGS for AMR surveillance

• What is missing from this?

– What population(s)?

– Pathogens are not the only important bugs

• Commensals, indicator organisms, microbiome


What are the objectives of AMR

surveillance?• Analysis of trends in AMR rates

• Frequency of AMR infections

• Impact of AMR infections on human

health?

• Data to inform antimicrobial categorization

and/or prudent use guidelines/systems

• Data for risk assessment/analysis

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What are the objectives of AMU

surveillance?• Analysis of trends in AMU rates

• Data for risk assessment/analysis

• Ideally linked to AMR data in some

manner

– Level of the population? Individual?

– Goal: understand selection pressure for AMR

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AMU Surveillance Objectives

• Where does this get complicated?

– Linking animal AMU to human AMR

– Linking individual AMU to individual/

population AMR

– Complicated drug distribution system

• Humans but especially animals

– What will you do with the data?

• Educate? Policy? Regulate use? (eg yellow card)

• At what level of the population? Census vs sample

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Integrated AMR/AMU Surveillance?

• What does “integrated” mean?

• For AMR and AMU surveillance,

integration means that data from multiple

sources/populations are analyzed to

understand how AMU affects AMR in the

complex “confusogram” system under

consideration

Many different possible “levels”

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Integrated AMR/AMU Surveillance?

• Sample sources (populations):

– Human specimens

– Food-animals

– Retail food

– Environment? Crops? Water? Soil?

• What is the objective of the program?

– Foodborne transmission?

– Nosocomial infection?

– Information? Education? Regulation?

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Target bacteria?

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Taken from the PHAC CARSS 2018 Stakeholder presentation – CARSS report 2017.

AMU Surveillance?

• Where, how, whither…?

• AMU data collection is complicated

• Level of collection depends on the level of

comparison

• Integration can take many forms

• There are many ways to measure AMU

– Total kg, mg/PCU, DDDvetCA/1000 ADR…

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AMR/AMU Surveillance

• Integrated AMR/AMU surveillance– This gets very granular very quickly…

• 2014 NCCID report – recommendations for Canada for

integrated surveillance– https://nccid.ca/publications/surveillance-of-antimicrobial-resistance-and-

antimicrobial-utilization-in-canada/

• 2016 CCVO report – AMU surveillance in animals– https://www.cahss.ca/media/uploads/cipars/documents/17-08-01_19-

44/CCVO_AMUCommittee_Non-HumanAMUSurveillance_FINAL_NjgJxTA.pdf

• Update on Canadian progress – CPHA Public Health 2020,

abstract (Miazga-Rodriguez/Saxinger/Otto)– https://youtu.be/PD7wGeA8hKU

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https://nccid.ca/publications/surveillance-of-antimicrobial-resistance-and-antimicrobial-utilization-in-canada/

https://www.cahss.ca/media/uploads/cipars/documents/17-08-01_19-44/CCVO_AMUCommittee_Non-HumanAMUSurveillance_FINAL_NjgJxTA.pdf

https://youtu.be/PD7wGeA8hKU

AMR and AMU Surveillance

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https://www.canada.ca

/content/dam/hc-

sc/documents/service

s/drugs-health-

products/canadian-

antimicrobial-

resistance-

surveillance-system-

2020-report/CARSS-

2020-report-2020-

eng.pdf

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https://www.canada.ca/content/dam/hc-sc/documents/services/drugs-health-products/canadian-antimicrobial-resistance-surveillance-system-2020-report/CARSS-2020-report-2020-eng.pdf

Dr. Ian Lewis

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Whole Genome SequencingWHO 2020 WGS: https://www.who.int/publications/i/item/9789240011007

• AMR surveillance still largely depends on

phenotypic testing

• Opportunities for metabolomics (Dr. Lewis)

• Opportunities for genomics and

metagenomics

• In silico and machine learning methods to

infer phenotype from genotype

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WGS Opportunities

• WGS – DNA sequence compared to

reference database

– Identify AMR genes

– Possibly identify virulence genes, promoters,

etc

– Reconstruction of transmission networks

based on molecular (genetic) subtypes

• Good from a One Health perspective

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WGS Opportunities

• Identify molecular determinants and

mechanisms of AMR

• Identify genetic factors facilitating

transmission of AMR genes within microbial

populations

• Useful addition to phenotypic at present

• Metagenomics – avoid the need for pure

culture = less time

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WGS Limitations

• WGS still requires a pure culture of an

organism

• WGS cannot completely substitute

phenotypic methods

– Genotype is not always = phenotype

Role for metabolomics

• Lack of international standards

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Metagenomics Limitations

• Long-read sequencing methods (next-

generation sequencing)

• Methods still not there, but improving!

– Error rates

– Bioinformatics

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Select Surveillance Examples

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Taken from the PHAC CARSS 2016 Stakeholder presentation – CARSS report 2016.

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30Taken from the CIPARS 2019 Stakeholder presentation – integrated 2018 results.


PCU (Population correction units) = biomass of animals in the population↑ 6%

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National comparisons of AMU:

Canada vs EU (mg/PCU)

Assumes that data are comparable

Taken from the CIPARS 2019 Stakeholder presentation – integrated 2018 results.

Taken from the CIPARS 2017 Stakeholder presentation – integrated 2016 results. 33


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Ceftriaxone-resistance in NTS


Highly Drug-resistant Salmonella

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Taken from the CIPARS 2017 Stakeholder presentation – integrated 2016 results.37


Co-selection gentamicin + lincomycin-spectinomycin useVeterinary Microbiology 203 (2017) 149–157

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http://www.bccdc.ca/health-professionals/data-reports/antimicrobial-resistance-utilization

http://www.bccdc.ca/health-professionals/data-reports/antimicrobial-resistance-utilization

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http://www.bccdc.ca/health-professionals/data-reports/antimicrobial-resistance-utilization/antimicrobial-resistance-dashboard

http://www.bccdc.ca/health-professionals/data-reports/antimicrobial-resistance-utilization/antimicrobial-resistance-dashboard

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http://www.bccdc.ca/health-professionals/data-reports/antimicrobial-resistance-utilization/antimicrobial-utilization-dashboard

http://www.bccdc.ca/health-professionals/data-reports/antimicrobial-resistance-utilization/antimicrobial-utilization-dashboard

Summary

• AMR and AMU surveillance must be

integrated to truly understand the links

between use and resistance

– This integration can be at different levels and

in different ways

– Surveillance program design depends on its

objectives

• There are One Health gaps in surveillance

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Thank you!

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microbial diagnostics - university of calgary in alberta

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