Antibiotic Resistance in Salmonella enterica Serovar Typhimurium Associates with CRISPR Sequence Type

Abstract

Salmonella enterica subsp. enterica serovar Typhimurium is a leading cause of food-borne salmonellosis in the United States. The number of antibiotic-resistant isolates identified in humans is steadily increasing, suggesting that the spread of antibiotic-resistant strains is a major threat to public health. S Typhimurium is commonly identified in a wide range of animal hosts, food sources, and environments, but little is known about the factors mediating the spread of antibiotic resistance in this ecologically complex serovar. Previously, we developed a subtyping method, CRISPR-multi-virulence-locus sequence typing (MVLST), which discriminates among strains of several common S. enterica serovars. Here, CRISPR-MVLST identified 22 sequence types within a collection of 76 S Typhimurium isolates from a variety of animal sources throughout central Pennsylvania. Six of the sequence types were identified in more than one isolate, and we observed statistically significant differences in resistance among these sequence types to 7 antibiotics commonly used in veterinary and human medicine, such as ceftiofur and ampicillin (P < 0.05). Importantly, five of these sequence types were subsequently identified in human clinical isolates, and a subset of these isolates had identical antibiotic resistance patterns, suggesting that these subpopulations are being transmitted through the food system. Therefore, CRISPR-MVLST is a promising subtyping method for monitoring the farm-to-fork spread of antibiotic resistance in S Typhimurium.

Fig 1

Graphic representation of spacer content for all CRISPR1 (A) and CRISPR2 (B) alleles identified in the ADL S. Typhimurium collection. Alleles marked in bold were also identified in the Fabre et al. isolate collection. A uniquely colored box and symbol combination designates each spacer sequence, and the shape of the symbol inside the box designates the length of the spacer. The ° symbol represents a truncated repeat that runs into an adjacent spacer, each of which is indistinguishable from the other. The box designated “IS” represents the position of IS10. Spacers have been aligned in order to facilitate comparison among alleles.

Fig 2

(A to C) Heat map showing the frequency of resistance to individual antibiotics by sequence type for ADL isolates and human clinical isolates combined (A), ADL isolates only (B), and clinical isolates only (C). (D) The frequencies of the most common antibiotic resistance patterns for ADL and human clinical isolates compared by sequence type. (E) Heat map key. Antibiotics are represented by the following abbreviations: Am, ampicillin; Ce, ceftiofur; Ch, chlortetracycline; Ge, gentamicin; Ne, neomycin; Ox, oxytetracycline; TS, trimethoprim-sulfamethoxazole.