Antibiotic-resistant commensal Escherichia coli are less frequently isolated from poultry raised using non-conventional management systems than from conventional broiler

Int J Food Microbiol. 2020 Feb 2;314:108391. doi: 10.1016/j.ijfoodmicro.2019.108391. Epub 2019 Oct 22.


Poultry production is the fastest growing meat sector worldwide. In the last five years, growing concerns have been expressed by international health agencies and consumers about the transmission of antibiotic-resistant bacteria from poultry meat to human. Consequently, poultry producers have adopted alternative production systems based on reduced antibiotic usage, including organic and antibiotic-free (AF) production. However, the effect of these production systems on the antibiotic resistance of the gut flora in slaughtered poultry has been poorly investigated. We hypothesized that organic and AF production systems reduce the risk of antibiotic resistance in the commensal Escherichia coli of broilers at slaughter compared with conventional production. Cecal content from broilers raised in conventional (292), AF (291), or organic (272) flocks (855 broilers in total) belonging to the same company was sampled. E. coli loads [colony-forming units (CFU/g)] and numbers of E. coli resistant to nalidixic acid (E. colinal) were determined for each sample. Antibiotic susceptibility of one isolate per sample was evaluated using the disc diffusion method; colistin resistance was determined by using the broth microdilution method. The differences in bacterial loads from the three production types were evaluated using one-way ANOVA. Differences in the proportion of resistant isolates in the three production lines were evaluated using Pearson's χ2 or Fisher's test. The strength of the association was evaluated by using odds ratio (OR), with the conventional production type as a reference (OR = 1). Overall, the analysis revealed a high level of resistance (50% or higher) to ampicillin, cefazolin, sulfonamides, nalidixic acid, and tetracycline, independently of the production type. High proportion of ciprofloxacin resistance (52%) was observed, with 4.5% isolates resistant to cefotaxime and 1.8% resistant to colistin. The average loads (log CFU/g cecal content) of E. colinal were determined as 6.84 for AF, 6.38 for organic type, and 7.27 for conventional type. The difference was significant (p < 0.00001). Interestingly, broilers from AF flocks had higher E. colinal loads than broilers from organic flocks. This trend (conventional > AF > organic) was confirmed by qualitative data. However, the magnitude of the effect, measured as a reduced risk of resistance, varied broadly for the antibiotics tested. These findings suggest that poultry production systems alternative to the conventional broiler production are associated with reduced frequency of antibiotic-resistant E. coli among the commensal gut flora, posing a lower risk to the environment and the consumer.

Keywords: Antibiotic resistance; Antibiotic-free; Farming; Organic.

Publication types

  • Comparative Study

MeSH terms

  • Agriculture / methods*
  • Animals
  • Anti-Bacterial Agents / administration & dosage
  • Anti-Bacterial Agents / pharmacology*
  • Cecum / microbiology
  • Chickens / microbiology
  • Drug Resistance, Bacterial*
  • Escherichia coli / drug effects*
  • Escherichia coli / growth & development
  • Escherichia coli / isolation & purification*
  • Escherichia coli Infections / microbiology
  • Escherichia coli Infections / veterinary*
  • Microbial Sensitivity Tests
  • Poultry / microbiology*


  • Anti-Bacterial Agents