Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) - Publications

On this page is a list of publications that include CIPARS authors. Publications that used CIPARS data are listed under “CIPARS publications” and those that did not use CIPARS data are listed under “CIPARS-affiliated publications”. Publications are listed by the year they were published beginning with the most recent.*

*This publication list is not exhaustive.

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CIPARS publications

Publication year Reference
2021 Agunos A, Gow SP, Deckert A, et al. Informing stewardship measures in Canadian food animal species through integrated reporting of antimicrobial use and antimicrobial resistance surveillance data—part I, Methodology development. Pathogens. 2021;10(11):1492 doi.org/10.3390/pathogens10111492.
2021 Agunos A, Gow SP, Deckert A, et al. Informing stewardship measures in Canadian food animal species through integrated reporting of antimicrobial use and antimicrobial resistance surveillance data—part II, Application. Pathogens. 2021;10(11):1491 doi.org/10.3390/pathogens10111491.
2021 Agunos A, Gow SP, Léger DF, et al. Antimicrobial resistance and recovery of Salmonella, Campylobacter, and Escherichia coli from chicken egg layer flocks in Canadian sentinel surveillance sites using 2 types of sample matrices. Can J Vet Res 2021;85:27-35 doi:cjvr_01_27 [pii].
2021 Bharat A, Murphy CP, Mulvey MR, et al. Antimicrobial-resistant nontyphoidal Salmonella infections, United States, 2004-2016. Emerg Infect Dis. 2021 Oct;27(10):2746 doi: 10.3201/eid2710.211339.
2021 Bosman A, Deckert A, Carson C, et al. Choosing which metrics to use when reporting antimicrobial use information to veterinarians in the Canadian swine industry. Can Vet J 2021;62:453-460.
2021 Tran T, Checkley S, Caffrey N, et al. Genetic characterization of AmpC and extended-spectrum beta-lactamase phenotypes in Escherichia coli and Salmonella from Alberta broiler chickens. Front Cell Infect Microbiol 2021;11:622195 doi:10.3389/fcimb.2021.622195 [doi].
2020 Agunos A, Gow S, Léger D, et al. Antimicrobial use indices—the value of reporting antimicrobial use in multiple ways using data from Canadian broiler chicken and turkey farms. Front Vet Sci 2020;7 doi:10.3389/fvets.2020.567872.
2020 Drame O, Leclair D, Parmley EJ, et al. Antimicrobial resistance of Campylobacter in broiler chicken along the food chain in Canada. Foodborne Pathog Dis 2020;17:512-20 doi:10.1089/fpd.2019.2752 [doi].
2019 Agunos A, Gow S, Léger D, et al. Antimicrobial use and antimicrobial resistance indicators - integration of farm-level surveillance data from broiler chickens and turkeys in British Columbia, Canada. Front Vet Sci 2019;6:131 doi: 10.3389/fvets.2019.00131.
2019 Agunos A, Deckert A, Léger D, et al. Antimicrobials used for the therapy of necrotic enteritis and coccidiosis in broiler chickens and turkeys in Canada, Farm Surveillance results (2013-2017). Avian Dis 2019;63:433-45 doi:10.1637/11971-091718-Reg.1 [doi].
2019 Bosman A, Loest D, Carson C, et al. Developing Canadian defined daily doses for animals: a metric to quantify antimicrobial use. Front in Vet Sci 2019;6:220 doi:10.3389/fvets.2019.00220.
2018 Agunos A, Arsenault RK, Avery BP, et al. Changes in antimicrobial resistance levels among Escherichia coli, Salmonella, and Campylobacter in Ontario broiler chickens between 2003 and 2015. Can J Vet Res 2018;82:163-77 doi:cjvr_07_163 [pii].
2018 MacKinnon MC, Pearl DL, Carson CA, et al. A comparison of modelling options to assess annual variation in susceptibility of generic Escherichia coli isolates to ceftiofur, ampicillin and nalidixic acid from retail chicken meat in Canada. Prev Vet Med 2018;160:123-35 doi:S0167-5877(17)30732-8 [pii].
2018 MacKinnon MC, Pearl DL, Carson CA, et al. Comparison of annual and regional variation in multidrug resistance using various classification metrics for generic Escherichia coli isolated from chicken abattoir surveillance samples in Canada. Prev Vet Med 2018;154:9-17 doi:S0167-5877(17)30798-5 [pii].
2017 Agunos A, Léger DF, Carson CA, et al. Antimicrobial use surveillance in broiler chicken flocks in Canada, 2013-2015. PLoS One 2017;12:e0179384 doi:10.1371/journal.pone.0179384 [doi].
2014 Agunos A, Léger DF, Avery BP, et al. Ciprofloxacin-resistant Campylobacter in broiler chicken in Canada. Can Commun Dis Rep 2014;40:36-41 doi:40S206 [pii].
2013 Agunos A. Antimicrobial therapy of bacterial diseases in broiler chickens - a reply. Can Vet J 2013;54:201-2 doi:cvj_03_201b [pii].
2013 Agunos A, Léger D, Avery BP, et al. Ciprofloxacin-resistant Campylobacter spp. in retail chicken, western Canada. Emerg Infect Dis 2013;19:1121-4 doi:10.3201/eid1907.111417 [doi].
2012 Nesbitt A, Ravel A, Murray R, et al. Integrated surveillance and potential sources of Salmonella enteritidis in human cases in Canada from 2003 to 2009. Epidemiol Infect 2012;140:1757-72 doi:S0950268811002548 [pii].
2010 Deckert A, Gow S, Rosengren L, et al. Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) Farm Program: results from finisher pig surveillance. Zoonoses Public Health 2010;57 Suppl 1:71-84 doi:10.1111/j.1863-2378.2010.01356.x [doi].
2010 Dutil L, Irwin RJ, Finley R, Ng LK, Avery BP, Boerlin P, et al. Ceftiofur Resistance in Salmonella enterica Serovar Heidelberg from Chicken Meat and Humans, Canada. Emerg Infect Dis. 2010;16(1):48-54. doi: 10.3201/eid1601.090729

CIPARS-affiliated publications

Publication Year Reference
2021 Caffrey N, Agunos A, Gow S, et al. Salmonella spp. prevalence and antimicrobial resistance in broiler chicken and turkey flocks in Canada from 2013 to 2018. Zoonoses Public Health 2021 doi:10.1111/zph.12769 [doi].
2021 Caffrey N, Agunos A, Gow S, et al. A cross-sectional study of the prevalence factors associated with fluoroquinolone resistant Campylobacter jejuni in broiler flocks in Canada. Prev Vet Med 2021;186:105164 doi:S0167-5877(20)30848-5 [pii].
2021 Collineau L, Carson CA, Moreno MA. Editorial: Antimicrobial usage in companion and food animals: methods, surveys and relationships with antimicrobial resistance in animals and humans, volume II. Front Vet Sci 2021;8:728267 doi:10.3389/fvets.2021.728267 [doi].
2021 Cox GW, Parmley EJ, Avery BP, et al. A one health genomic investigation of gentamicin resistance in Salmonella from human and chicken sources in Canada, 2014-2017. Antimicrob Agents Chemother. 2021 Sep 27:AAC0096621 doi: 10.1128/AAC.00966-21.
2021 Ghosh KK, Janecko N, Agunos A, et al. Evaluation of selective media in antimicrobial surveillance programs capturing broad-spectrum β-lactamase producing Escherichia coli from chickens at slaughter. Can Vet J 2021;62:608-10 doi:cvj_06_608 [pii].
2021 Huber, L.; Agunos, A.; Gow, S.P.; Carson, C.A.; Van Boeckel, T.P. Reduction in antimicrobial use and resistance to Salmonella, Campylobacter, and Escherichia coli in broiler chickens, Canada, 2013–2019. Emerg. Infect. Dis. 2021, 27, 2434–2444, doi:10.3201/eid2709.204395.
2021 Léger A, Lambraki I, Graells T, et al. AMR-Intervene: a social-ecological framework to capture the diversity of actions to tackle antimicrobial resistance from a One Health perspective. J Antimicrob Chemother 2021;76 doi:10.1093/jac/dkaa394.
2021 McDonald KL, Garland S, Carson CA, et al. Measures used to assess the burden of ESBL-producing Escherichia coli infections in humans: a scoping review. JAC Antimicrob Resist 2021;3:dlaa104 doi:10.1093/jacamr/dlaa104 [doi].
2020 Collineau L, Chapman B, Bao X, et al. A farm-to-fork quantitative risk assessment model for Salmonella Heidelberg resistant to third-generation cephalosporins in broiler chickens in Canada. Int J Food Microbiol 2020;330:108559 doi:S0168-1605(20)30053-2 [pii].
2020 MacKinnon MC, Sargeant JM, Pearl DL, et al. Evaluation of the health and healthcare system burden due to antimicrobial-resistant Escherichia coli infections in humans: a systematic review and meta-analysis. Antimicrob Resist Infect Control 2020;9:200 doi:10.1186/s13756-020-00863-x [doi].
2020 Moffat J, Chalmers G, Reid-Smith R, et al. Resistance to extended-spectrum cephalosporins in Escherichia coli and other Enterobacterales from Canadian turkeys. PLoS One 2020;15:e0236442 doi:10.1371/journal.pone.0236442 [doi].
2020 Moreno MA, Collineau L, Carson CA. Editorial: Antimicrobial usage in companion and food animals: methods, surveys and relationships with antimicrobial resistance in animals and humans. Front Vet Sci 2020;7:63 doi:10.3389/fvets.2020.00063 [doi].
2020 Racicot M, Comeau G, Leroux A, et al. Expert elicitation to estimate the relative risk of food safety criteria included in the establishment-based risk assessment model for Canadian hatcheries. Foodborne Pathog Dis 2020;17:641-65 doi:10.1089/fpd.2019.2784 [doi].
2020 Racicot M, Comeau G, Tremblay A, et al. Identification and selection of food safety-related risk factors to be included in the Canadian Food Inspection Agency's Establishment-based Risk Assessment model for Hatcheries. Zoonoses Public Health 2020;67:14-24 doi:10.1111/zph.12650 [doi].
2020 Romero-Barrios P, Deckert A, Parmley E, et al. Antimicrobial resistance profiles of Escherichia coli and Salmonella isolates in Canadian broiler chickens and their products. Foodborne pathogens and disease 2020;17 doi: 10.1089/fpd.2019.2776.
2020 Sanders P, Vanderhaeghen W, Fertner M, et al. Monitoring of farm-level antimicrobial use to guide stewardship: overview of existing systems and analysis of key components and processes. Front Vet Sci 2020;7:540 doi:10.3389/fvets.2020.00540 [doi].
2020 Wernli D, Jørgensen P, Parmley E, et al. Evidence for action: a One Health learning platform on interventions to tackle antimicrobial resistance. Lancet Infect Dis 2020;12:e307-e311 doi: 10.1016/S1473-3099(20)30392-3.
2019 Carson C, Li XZ, Agunos A, et al. Ceftiofur-resistant Salmonella enterica serovar Heidelberg of poultry origin - a risk profile using the Codex framework. Epidemiol Infect 2019;147:e296 doi:10.1017/S0950268819001778 [doi].
2019 Collineau L, Boerlin P, Carson CA, et al. Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges. Front Microbiol 2019;10:1107 doi:10.3389/fmicb.2019.01107 [doi].
2019 Collineau L, Phillips C, Chapman B, et al. A within-flock model of Salmonella Heidelberg transmission in broiler chickens. Preventive veterinary medicine 2019;174 doi: 10.1016/j.prevetmed.2019.104823.
2019 Cormier A, Zhang PLC, Chalmers G, et al. Diversity of CTX-M-positive Escherichia coli recovered from animals in Canada. Vet Microbiol 2019;231:71-5 doi:S0378-1135(19)30005-7 [pii].
2018 Chalmers G, Davis KE, Poljak Z, et al. A method to detect Escherichia coli carrying the colistin-resistance genes mcr-1 and mcr-2 using a single real-time polymerase chain reaction and its application to chicken cecal and porcine fecal samples. Can J Vet Res 2018;82:312-5.
2018 Lebert L, Martz SL, Janecko N, et al. Prevalence and antimicrobial resistance among Escherichia coli and Salmonella in Ontario smallholder chicken flocks. Zoonoses Public Health 2018;65:134-41 doi:10.1111/zph.12381 [doi].
2018 Majowicz SE, Parmley E, Carson C, et al. Identifying non-traditional stakeholders with whom to engage, when mitigating antimicrobial resistance in foodborne pathogens (Canada). BMC Research Notes 2018;11 doi:10.1186/s13104-018-3279-8.
2018 Murphy C, Carson C, Smith BA, et al. Factors linked with the occurrence of antimicrobial resistance in cattle, chickens, and pigs: A qualitative review of publications for use in integrated assessment modelling of antimicrobial resistance (IAM.AMR Project). Zoonoses and Public Health 2018;65:957-971 doi:10.1111/zph.12515.
2018 Nekouei O, Checkley S, Waldner C, et al. Exposure to antimicrobial-resistant Escherichia coli through the consumption of ground beef in Western Canada. International journal of food microbiology 2018;272:41-48 doi:10.1016/j.ijfoodmicro.2018.02.022.
2017 Caffrey N, Nekouei O, Gow S, et al. Risk factors associated with the A2C resistance pattern among E. coli isolates from broiler flocks in Canada. Prev Vet Med 2017;148:115-20 doi:S0167-5877(17)30252-0 [pii].
2016 Labbé G, Ziebell K, Bekal S, et al. Complete genome sequences of 17 Canadian isolates of Salmonella enterica subsp. enterica serovar Heidelberg from human, animal, and food sources. Genome Announc 2016;4:e00990,16. doi: 10.1128/genomeA.00990-16 doi:10.1128/genomeA.00990-16 [doi].
2016 Narvaez-Bravo C, Toufeer M, Weese SJ, et al. Prevalence of methicillin-resistant Staphylococcus aureus in Canadian commercial pork processing plants. J Appl Microbiol 2016;120:770-80 doi:10.1111/jam.13024 [doi].
2014 Deckert AE, Taboada E, Mutschall S, et al. Molecular epidemiology of Campylobacter jejuni human and chicken isolates from two health units. Foodborne Pathog Dis 2014;11:150-5 doi:10.1089/fpd.2013.1610 [doi].
2013 Agunos A, Carson C, Léger D. Antimicrobial therapy of selected diseases in turkeys, laying hens, and minor poultry species in Canada. Can Vet J 2013;54:1041-52 doi:cvj_11_1041 [pii].
2013 Deckert AE, Reid-Smith RJ, Tamblyn S, et al. Burden of illness and factors associated with duration of illness in clinical campylobacteriosis. Epidemiol Infect 2013;141:2536-46 doi:10.1017/S0950268813000332 [doi].
2013 Deckert AE, Reid-Smith RJ, Tamblyn SE, et al. Antimicrobial resistance and antimicrobial use associated with laboratory-confirmed cases of Campylobacter infection in two health units in Ontario. Can J Infect Dis Med Microbiol 2013;24:e16-21 doi:10.1155/2013/176494 [doi].
2012 Agunos A, Léger D, Carson C. Review of antimicrobial therapy of selected bacterial diseases in broiler chickens in Canada. Can Vet J 2012;53:1289-300 doi:cvj_12_1289 [pii].
2011 Weese JS, Rousseau J, Deckert A, et al. Clostridium difficile and methicillin-resistant Staphylococcus aureus shedding by slaughter-age pigs. BMC Vet Res 2011;7:41,6148-7-41 doi:10.1186/1746-6148-7-41 [doi].
2010 Deckert A, Valdivieso-Garcia A, Reid-Smith R, et al. Prevalence and antimicrobial resistance in Campylobacter spp. isolated from retail chicken in two health units in Ontario. J Food Prot 2010;73:1317-24 doi:10.4315/0362-028x-73.7.1317 [doi].
2009 Valdivieso-Garcia A, Imgrund R, Deckert A, et al. Cost analysis and antimicrobial susceptibility testing comparing the E test and the agar dilution method in Campylobacter jejuni and Campylobacter coli. Diagn Microbiol Infect Dis 2009;65:168-74 doi:10.1016/j.diagmicrobio.2009.07.008 [doi].
2009 Waddell L, Rajic A, Sargeant J, et al. The methodological soundness of literature reviews addressing three potential zoonotic public health issues. Zoonoses Public Health 2009;56:477-89 doi:10.1111/j.1863-2378.2008.01194.x [doi].
2008 Avery BP, Rajic A, McFall M, et al. Antimicrobial use in the Alberta sheep industry. Can J Vet Res 2008;72:137-42.
2007 Rajic A, Chow EY, Wu JT, et al. Salmonella infections in ninety Alberta swine finishing farms: serological prevalence, correlation between culture and serology, and risk factors for infection. Foodborne Pathog Dis 2007;4:169-77 doi:10.1089/fpd.2006.0073 [doi].
2007 Rajic A, Keenliside J, McFall ME, et al. Longitudinal study of Salmonella species in 90 Alberta swine finishing farms. Vet Microbiol 2005;105:47-56 doi:S0378-1135(04)00361-X [pii].
2007 Rajic A, O'Connor BP, Deckert AE, et al. Farm-level risk factors for the presence of Salmonella in 89 Alberta swine-finishing barns. Can J Vet Res 2007;71:264-70.
2007 Valdivieso-Garcia A, Harris K, Riche E, et al. Novel Campylobacter isolation method using hydrophobic grid membrane filter and semisolid medium. J Food Prot 2007;70:355-62 doi:10.4315/0362-028x-70.2.355 [doi].
2006 Rajic A, Reid-Smith R, Deckert AE, et al. Reported antibiotic use in 90 swine farms in Alberta. Can Vet J 2006;47:446-52.
2004 Rajic A, McFall ME, Deckert AE, et al. Antimicrobial resistance of Salmonella isolated from finishing swine and the environment of 60 Alberta swine farms. Vet Microbiol 2004;104:189-96 doi:S0378-1135(04)00336-0 [pii].
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