2018-19 Rapid Ag: Characterization of emergent antimicrobial resistance in Salmonella strains residing at the animal-human interface to guide evidence-based antimicrobial stewardship in veterinary medicine

April 3, 2017

Principle Leader

Dr. Julio Alvarez


Department of Veterinary Population Medicine

Funding Awarded

Fiscal Year 2018: $113,700

The Problem

Although first described shortly after the introduction of antimicrobials in the 1940s, the emergence of antimicrobial resistance (AMR) has been recently identified as one of the most important challenges that mankind needs to face in the 21st century (1). AMR genes were present in nature long before the “antibiotic era, but the use of antimicrobials has contributed to selection of resistant strains through enrichment and evolution of resistance genes, leading to the current threat.


Salmonella, one of the major causes of foodborne illness in the United States, exemplifies the need for considering the human-animal-environment interface for disease control and prevention due to the multiple sources of infection for humans that have been described (including multiple foods of animal origin and produce) (7). Although salmonellosis is often self-limiting and does not require antibiotic treatment, it can also be invasive and potentially fatal, particularly for children, elderly and immunocompromised patients (8). In such cases, effective antibiotic therapy is crucial but will be compromised by the presence of resistant isolates. Treatment in humans typically involves use of thirdgeneration cephalosporins and fluoroquinolones (8), and for this reason the increased resistance against members of these antibiotic classes (ceftriaxone and ciprofloxacin, respectively) observed in the last decade is particularly concerning (9). Use of antibiotics in food animals has been considered one of the major factors driving the increased resistance in human Salmonella isolates (10). This is supported through data recovered at the Minnesota Veterinary Diagnostic Laboratory (MVDL) demonstrating an increase (from ~0% in 2008 to ~20% in 2015) in the proportion of swine clinical isolates resistant to enrofloxacin (a fluoroquinolone antibiotic licensed for use in swine in the United States in 2008) (11). A preliminary analysis on a subset of those enrofloxacin-resistant isolates using whole genome sequencing (WGS) demonstrated that all harbored plasmid-mediated quinolone resistance (PMQR) qnr genes (Elnekave et al., in preparation), and a recent study showing that presence of qnr genes was associated with decreased susceptibility to fluoroquinolones in US human isolates (12). These qnr genes have been also recently reported for the first time in the United States in Salmonella isolated from retail meat (in 2014) (13) and in food animals (cattle, 2016) (14), and represent a particular concern due to their potential for transmissibility among Salmonella. Although percentages of fluoroquinolone-resistant strains of human origin has remained low (<5% according to NARMS data) the increase observed in the last decade, coupled with the increase in the proportion of human isolates harboring PMQR mechanisms compared with the 1996-2003 period (15), provides additional evidences of a complex emergent problem that can be further complicated due to the potential for co-transmission and co-selection of PMQR with other resistance mechanisms such as extended spectrum β-lactamases or carbapenemases in Salmonella and other gram-negative bacteria (16). Selection pressure due to routine use of cephalosporin in swine was also hypothesized as the selective force behind the recent finding of carbapenemase-producing Enterobacteriaceae (CRE) from the environment of a swine operation in the US (17).

In this context, characterizing the dynamics of antimicrobial use and AMR spread in animals is critical in order to evaluate the importance of food animals as sources or reservoirs of AMR genes and AMR bacteria and to guide evidence-based antimicrobial stewardship in veterinary medicine. Unfortunately, there is limited information on the potential usefulness of stopping antibiotic use as an strategy for reducing AMR, with several studies suggesting that it can lead to a reduction of the prevalence of resistant strains but may not lead to its elimination (18). Particularly lacking is an understanding of the genetics behind resistant phenotypes, which is critical to establish the corresponding fitness cost associated with it. Techniques with very high discriminatory power are required to establish the relationship between isolates from different sources, an aspect particularly important for outbreak investigation in the case of Salmonella and that can help to identify emergent clones and the potential virulence mechanisms behind their emergence. Whole genome sequencing (WGS) can help to address these issues, since i) detection of AMR determinants through WGS has been demonstrated to correlate very well with phenotypic resistance in Salmonella (12); and ii) when applied to both human and animal isolates, WGS can enable estimation of the degree of inter-species transmission of dominant clones (19). Successful completion of this project will result in the identification of AMR mechanisms shared by Salmonella isolates of both animal and human origins and provide information for a precise and datadriven assessment of the situation, which will, in the short term, help to: 

  • Evaluate the possible role of animals as sources of multidrug resistant isolates as human pathogens and as vectors of AMR mobile determinants through the analysis of a large collection of animal isolates coming from different species (and subjected to different antimicrobial selective pressures).
  • Evaluate the possible effect of veterinary use of cephalosporins and fluoroquinolones, as well as other antimicrobials, in the selection of predominant AMR Salmonella clones and/or diverse strains harboring shared AMR determinants in different food animal systems based on the nature and location of those determinants and the different use of these drugs depending on the species.
  • Assess the risk of co-resistance to cephalosporins and fluoroquinolones in human and animal Salmonella strains
  • Generate evidence for raising awareness on the consequences of use of antimicrobials in veterinary medicine from both animal health (decrease in efficacy of antibiotic treatments) and public health (contribution to the AMR) perspectives In the long term, this information can be used as a baseline in future studies to evaluate the usefulness of current antimicrobial stewardship efforts in veterinary medicine, and to detect the emergence of new resistant clones/determinants in Salmonella (and other bacteria).


The project will characterize antimicrobial resistance determinants, with a focus on those related to cephalosporins and fluoroquinolone resistance, present in Salmonella serotypes of human and animal origin and of most relevance for public and animal health. Using records of isolates of animal and human origin collected in Minnesota over the last 10 years, serotypes will be selected based on increasing incidence in human and/or animals, and high prevalence of multi-drug resistant phenotypes based on antimicrobial susceptibility testing. More specifically, we will:

  1. Identify all chromosomal and plasmid-mediated resistance genes against antibiotics of veterinary and human use present in Salmonella isolates of human and food animal origin collected through the Minnesota Department of Health and Minnesota Veterinary Diagnostic Laboratory, respectively.
  2. Evaluate the risk of co-selection of resistance to multiple antimicrobial/antimicrobial classes through the sequencing of plasmids potentially encoding several AMR determinants
  3. Assess the intra and inter-species variability with regards to antimicrobial resistance (AMR) determinants in order to evaluate the potential role of animals as source of both pathogenic and/or drug resistant Salmonella as well as plasmid-mediated AMR genes
  4. Disseminate findings from aims 1-3 to help effective evidence-based antimicrobial stewardship in veterinary practice through on-line educational materials for producers, veterinary students and veterinarians. This will include a discussion of resistance elements, development of resistance, and effects of antibiotic use under different circumstances (chromosomal/plasmid-mediated AMR genes, coselection of resistances) based on the findings (nature and presence of AMR determinants).


  1. National action plan for combating antibiotic-resistant bacteria.The White House.; 2015.
  2. Review on AMR: Antimicrobials in agriculture and the environment: reducing unnecessary use and waste; 2015.
  3. Singer RS et al. Lancet Infect Dis. 2003 Jan;3(1):47-51.
  4. FAO. Drivers, dynamics and epidemiology of antimicrobial resistance in animal production; 2016.
  5. Aarestrup FM et al. Expert Rev Anti Infect Ther. 2008 Oct;6(5):733-50.
  6. Landers TF et al. Public Health Rep. 2012 Jan-Feb;127(1):4-22.
  7. CDC. An atlas of Salmonella in the United States, 1968-2011. 2013;Atlanta, Georgia.
  8. Crump JA et al. Clin Microbiol Rev. 2015 Oct;28(4):901-37.
  9. Medalla F et al. 2013 Apr;10(4):302-9.
  10. Angulo FJ et al. J Vet Med B. 2004 Oct-Nov;51(8-9):374-9.
  11. Hong S et al. PloS one. 2016;11(12):e0168016.
  12. McDermott PF et al. Antimicrob Agents Chemother. 2016 Sep;60(9):5515-20.
  13. FDA. NARMS Retail Meat Interim Report for Salmonella Shows Encouraging Early Trends Continue; 2016.
  14. Cummings KJ et al. Zoonoses Public Health. 2016 Nov 01.
  15. CDC. NARMS: human isolates final report, 2013. Atlanta, Georgia; 2015.
  16. Robicsek A et al. Lancet Infect Dis. 2006 Oct;6(10):629-40.
  17. Mollenkopf DF et al. Antimicrob Agents Chemother. 2016 Dec 05.
  18. Melnyk AH et al. Evol Appl. 2015 Mar;8(3):273-83.
  19. Mather AE et al. Science. 2013 Sep 27;341(6153):1514-7.
  20. Earle SG et al. Nat Microbiol. 2016 Apr 04;1:16041.
  21. Alvarez J et al. Preventive veterinary medicine. 2016 Jan 01;123:155-60.
  22. Gordoncillo MJ et al. J Vet Med Educ. 2011 Winter;38(4):404-7.