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Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS): Design and methods

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Using whole genome sequencing for antimicrobial resistance prediction for Salmonella

CIPARS is transitioning from using broth microdilution to whole genome sequencing (WGS) for antimicrobial resistance (AMR) determination. With WGS, AMR is predicted based on the presence of genes, as compared to broth microdilution which measures the growth of bacteria in the presence of increasing concentrations of antimicrobials. Validation tests performed by the National Microbiology Laboratory found that the prediction of AMR from WGS for Salmonella is accurate and reliable (Bharat et al., 2022).

With this transition comes changes in how CIPARS reports ciprofloxacin resistance in Salmonella. With broth microdilution bacteria are classified as either susceptible, intermediate, or resistant depending on the lowest concentration of antimicrobial needed to inhibit growth. However, with WGS, the ciprofloxacin "resistance" genes do not discriminate between "resistant" and "intermediate", and findings are therefore reported as 1) "non-susceptible" (intermediate and resistant classification based on the presence of resistance genes) or 2) "susceptible" (based on the absence of resistance genes).

It is important to note that the percentage of ciprofloxacin "non-susceptible" Salmonella (determined using WGS) may be higher than in previous reports where the percentage of ciprofloxacin "resistant" Salmonella (determined using broth microdilution) was reported (Figure 1). Going forward, a component of this transition will include harmonizing WGS data with previous broth microdilution data for comparison of historical trends with current AMR surveillance findings.

Figure 1. Example comparing the reporting of findings from broth microdilution compared to whole genome sequences.
Figure 1. Text version below.
Figure 1 - Text description
Example comparing the reporting of findings from broth microdilution compared to whole genome sequences.
Method Findings Percentage of susceptible isolates Percentage of intermediate isolates Percentage of resistant isolates
Broth microdilution Susceptible 70 20 NA
Resistant NA NA 10
Whole genome sequencing Susceptible 70 NA NA
Non-susceptible NA 20 10
Not applicable: NA

Work cited:

Bharat A, Petkau A, Avery BP, Chen JC, Folster JP, Carson CA, Kearney A, Nadon C, Mabon P, Thiessen J, Alexander DC, Allen V, El Bailey S, Bekal S, German GJ, Haldane D, Hoang L, Chui L, Minion J, Zahariadis G, Domselaar GV, Reid-Smith RJ, Mulvey MR. Correlation between phenotypic and In Silico detection of antimicrobial resistance in Salmonella enterica in Canada using Staramr. Microorganisms. 2022;10(2):292 doi:10.3390/microorganisms10020292.

Recent Design and Methods document

This document describes the design and methods used for all antimicrobial resistance and antimicrobial use surveillance components for a recent surveillance year

All Design and Methods documents

These documents describe the design and methods used for all antimicrobial resistance and antimicrobial use surveillance components for all surveillance years, since the beginning of CIPARS in 2002

Surveillance year Document title
2019 2019 Design and Methods
2018 2018 Design and Methods
2017 2017 Design and Methods
2016 2016 Design and Methods: see Chapter 5 in the 2016 Annual Report
2015 2015 Design and Methods: see Chapter 5 in the 2015 Annual Report
2014 2014 Design and Methods: see Appendix in the 2014 Annual Report
2013 2013 Design and Methods: see the 2013 Chapter 1. Design and Methods
2012 2012 Design and Methods: see the 2012 Chapter 1. Design and Methods
2011 2011 Design and Methods: no annual report was published in 2011
2010 2010 Design and Methods: see Appendix A in the 2010 Annual Report
2009 2009 Design and Methods: see Appendix A in the 2009 Annual Report
2008 2008 Design and Methods: see Appendix A in the 2008 Annual Report
2007 2007 Design and Methods: see Appendix A in the 2007 Annual Report
2006 2006 Design and Methods: see Appendix A in the 2006 Annual Report
2005 2005 Design and Methods: see Appendix A in the 2005 Annual Report
2004 2004 Design and Methods: see Appendix B in the 2004 Annual Report
2003 2003 Design and Methods: see Appendix B in the 2003 Annual Report
2002 2002 Design and Methods: see Appendix B in the 2002 Annual Report

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To obtain additional information, please contact us by email: cipars-picra@phac-aspc.gc.ca

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