Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic

Abstract

Industrial farms are unique, human-created ecosystems that provide the perfect setting for the development and dissemination of antibiotic resistance. Agricultural antibiotic use amplifies naturally occurring resistance mechanisms from soil ecologies, promoting their spread and sharing with other bacteria, including those poised to become endemic within hospital environments. To better understand the role of enterococci in the movement of antibiotic resistance from farm to table to clinic, we characterized over 300 isolates of Enterococcus cultured from raw chicken meat purchased at U.S. supermarkets by the Consumers Union in 2013. Enterococcus faecalis and Enterococcus faecium were the predominant species found, and antimicrobial susceptibility testing uncovered striking levels of resistance to medically important antibiotic classes, particularly from classes approved by the FDA for use in animal production. While nearly all isolates were resistant to at least one drug, bacteria from meat labeled as raised without antibiotics had fewer resistances, particularly for E. faecium Whole-genome sequencing of 92 isolates revealed that both commensal- and clinical-isolate-like enterococcal strains were associated with chicken meat, including isolates bearing important resistance-conferring elements and virulence factors. The ability of enterococci to persist in the food system positions them as vehicles to move resistance genes from the industrial farm ecosystem into more human-proximal ecologies.IMPORTANCE Bacteria that contaminate food can serve as a conduit for moving drug resistance genes from farm to table to clinic. Our results show that chicken meat-associated isolates of Enterococcus are often multidrug resistant, closely related to pathogenic lineages, and harbor worrisome virulence factors. These drug-resistant agricultural isolates could thus represent important stepping stones in the evolution of enterococci into drug-resistant human pathogens. Although significant efforts have been made over the past few years to reduce the agricultural use of antibiotics, continued assessment of agricultural practices, including the roles of processing plants, shared breeding flocks, and probiotics as sources for resistance spread, is needed in order to slow the evolution of antibiotic resistance. Because antibiotic resistance is a global problem, global policies are needed to address this threat. Additional measures must be taken to mitigate the development and spread of antibiotic resistance elements from farms to clinics throughout the world.

Keywords: Enterococcus; agriculture; antibiotic resistance; antimicrobial resistance; food safety; molecular epidemiology; poultry; resistance; virulence.

FIG 1

CUE isolates were primarily E. faecalis and E. faecium. (A) Breakdown of all 333 CUE isolates by species (determined by 16S rRNA gene sequencing). See Table S1 for strain counts for each species. (B) Whole-genome phylogeny of 92 newly sequenced CUE isolates, in the context of additional previously published strains (13). Abx, antibiotics.

FIG 2

Resistance to drugs that are medically relevant for humans was common. Drug names shown in red are part of antibiotic classes used in animal rearing, except tigecycline and chloramphenicol; tigecycline and chloramphenicol are not used in animal rearing, but drugs from the same classes as these are used in animal rearing. Abx, antibiotics.

FIG 3

E. faecium isolates from chickens raised without antibiotics had significantly less phenotypic resistance than those from chickens raised conventionally. The difference was not significant for E. faecalis. The number of bacterial samples in each category is shown in parentheses. P values were computed using a two-sided Student t test.

FIG 4

The increase in resistance in E. faecium from chickens grown conventionally is due to broadly higher resistance to drugs used in animal rearing, including seven medically important drugs (highlighted in yellow). Antibiotics in red represent drugs used in animal rearing, and antibiotics with an asterisk represent those in the same class as drugs used in animal rearing.

FIG 5

Expanded species-specific phylogenies. (A) E. faecalis phylogeny including 32 newly sequenced CUE isolates, together with 149 additional E. faecalis strains (Table S4). (B) E. faecium phylogeny, including 43 newly sequenced CUE isolates, together with 73 previously published strains reported in Lebreton et al. (13) (Table S4).