Selection of Multidrug-Resistant Bacteria in Medicated Animal Feeds.

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PubMed ID: 30894847

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Brown EEF, Cooper A, Carrillo C, Blais B

Front Microbiol. 2019. doi: 10.3389/fmicb.2019.00456

COMMENT Foodborne outbreaks caused by antimicrobial resistant (AMR) bacteria are an important problem. Animal feeds are supplemented with antibiotics for growth-promotion and prophylaxis. To reduce the risk of fostering the development of antimicrobial resistance to medically important antibiotics the tendency has been to use non-priority antibiotics. However, for multi-drug resistant (MDR) bacteria, the application of this selective pressure may result in co-selection of other resistance genes present in the cell. This study focused on obtaining preliminary evidence of co-selection of medically relevant antimicrobial resistances occurring in an multi-drug resistant bacterial strain in medicated feeds.


We were interested in studying co-selection of a medically important resistance trait in an environmental MDR bacterial species capable of entering the food production chain (e.g., via animal feeds), under selection conditions involving the presence of a typical antibiotic used in commercially medicated feeds. For this purpose, we designated an MDR K. pneumoniae isolate recovered from raw sewage influent as a model for a naturally occurring environmental bacterium with the potential to serve as a reservoir for the transfer of AMR genes to the food animal microbiome. (…). A key objective of this study was to determine if this strain could be enriched after incubation under different conditions in animal feeds containing sulfadiazine, and also, whether the enriched bacteria carried both sulfonamide and meropenem resistance genes.

Main results

Whole genome sequence analysis of Klebsiella pneumoniae strains OLC-1237 (non-resistant control) and OLC-2685 (multi-drug resistant strain) was performed to determine the presence of antimicrobial resistant genes and confirm the bacterial species identity. Sequencing was performed on the Illumina MiSeq platform.

Genomic analysis of strain OLC-2685 determined the presence of multiple copies of sul1 (though their location on the chromosome or plasmids could not be ascertained) and that the blaPKC-3 gene was located on the Klebsiella plasmid pRYCKPC3.1, which did not contain a sul1 gene, indicating that the two genes were not genetically linked.

Genomic signature sequences were determined for the development of strain-specific PCR methods targeting the blaKPC-3 and Sul1 resistance genes found in Klebsiella pneumoniae OLC-2685 strain.

The enrichment of model multi-drug resistant and sulfonamide-sensitive K. pneumoniae strains in feeds non-medicated (having unselected background microbiota) was evaluated. For these experiments sulfadiazine was used as a typical representative of the sulfonamide family of antibiotics. Two main results were obtained from these experiments:

 (1) the presence of sulfadiazine in a feed sample imposes selective pressure which favors the outgrowth of K. pneumoniae (and possibly other bacteria) possessing resistance associated with Sul1, even in the presence of high levels of background bacteria. (2) selection on the basis of a single resistance trait causes co-selection of other traits present in the same cell, such as the gene specifying carbapenem resistance, even though the gene resides on a separate genetic element (plasmid).

The enrichment of the two strains was also determined in a commercially medicated feed under nutritionally limited and moist conditions with the following result:

selection of sulfonamide-resistant bacteria can occur under simulated feed storage conditions of high temperature and humidity that are propitious for microbial growth even in the absence of nutrient-rich media.


We have effectively demonstrated that selection and enrichment of AMR bacteria can occur in feeds, and most significantly, even when feeds are medicated with antibiotics not used in human medicine co-selection of resistance to clinically significant antibiotics can occur for bacterial strains harboring multiple resistance traits.

Animal feeds are immensely variable in terms of their ingredient composition, background bacteria profiles, storage and handling conditions, and any or all of these factors may impact the extent to which selection and enrichment of AMR bacteria might occur. However, we observed significant recovery of the MDR model strain under different conditions even with a small sampling of randomly acquired feeds. 


Diana López-Farfán