Antimicrobial resistance genes, cassettes, and plasmids present in Salmonella enterica associated with United States food animals

Authors: MCMILLAN, ELIZABETH - University Of Georgia; GUPTA, SUSHIM - Orise Fellow; WILLIAMS, LAURA - Providence College; JOVE, THOMAS - Inserm University Of Limoges; Hiott, Lari; Woodley, Tiffanie; Barrett, John; Jackson, Charlene; WASILENKO, JAMIE - Food Safety Inspection Service (FSIS); SIMMONS, MUSTAFA - Food Safety Inspection Service (FSIS); TILLMAN, GLENN - Food Safety Inspection Service (FSIS); MCCLELLAND, MICHAEL - University Of California; Frye, Jonathan

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2019
Publication Date: 4/17/2019
Citation: McMillan, E., Gupta, S., Williams, L., Jove, T., Hiott, L.M., Woodley, T.A., Barrett, J.B., Jackson, C.R., Wasilenko, J., Simmons, M., Tillman, G., McClelland, M., Frye, J.G. 2019. Antimicrobial resistance genes, cassettes, and plasmids present in Salmonella enterica associated with United States food animals. Frontiers in Microbiology. 10:832. https://doi.org/10.3389/fmicb.2019.00832.
DOI: https://doi.org/10.3389/fmicb.2019.00832

Interpretive Summary: Salmonella is one of the most prevalent food borne bacterial pathogens causing an estimated 1.3 Million human infections each year in the USA. Salmonella infections resistant to antibiotic treatment have been increasing. Salmonella becomes resistant to antibiotics by acquiring genes encoding resistance mechanisms to antibiotics. These genes can be transferred to Salmonella on mobile genetic elements which may have one or several resistance genes. The most common of these mobile elements are called plasmids, which are small, self-replicating, pieces of DNA that can be transfered from one bacteria to another through mating. Our understanding of these plasmids is limited and even less is known about their prevalence in food-animals. To fill this data gap almost 200 antibiotic resistant Salmonella isolated from food-animals were analyzed for plasmids and antibiotic resistance genes by whole genome sequencing. Analysis of this data determined that a variety of different types of plasmids were present in these Salmonella and almost all of the antibiotic resistance genes were found on plasmids. Further analysis showed common arrangements of these antibiotic resistance genes were found on many different types of plasmids. These gene arrangements were called "cassettes" because identical genes were found in many different plasmids as if a cassette had been inserted into them. Six cassettes were identified in this study and when compared to the database of all Salmonella whole genome sequences, many of them were found to be widespread in isolates from other studies. This improves our understanding of antibiotic resistance in Salmonella associated with food animals and can help us understand how they become resistant and could pose a threat to human health.

Technical Abstract: The ability of antibiotic resistance (AR) to transfer between bacteria on mobile genetic elements (MGEs) can cause the rapid establishment of multidrug resistance (MDR) in bacteria from animals leading to a foodborne risk to human health. To investigate MDR and its association with plasmids in Salmonella, whole genome sequence (WGS) analysis was performed on 193 S. enterica isolated from U.S. food animals, 118 of which were resistant to at least one antibiotic tested. Isolates represented 86 serovars and variants, as well as diverse phenotypic resistance profiles. Salmonella in this study were isolated from 1998 to 2011. This analysis identified a total of 923 AR genes and 212 plasmids among the 193 strains. Every isolate contained at least one AR gene and at least one plasmid was detected in 155 isolates. Genes were identified for resistance to aminoglycosides (n=462), ß-lactams (n=85), tetracyclines (n=171), sulfonamides (n=91), phenicols (n=42), trimethoprim(n=8), macrolides(n=5), fosfomycin (n=48), and rifampicin(n=2). The plasmid replicon types detected in the isolates were A/C (n=32), colE (n=76), F (n=43), HI1 (n=4), HI2 (n=20), I1 (n=62), N (n=4), Q (n=7), and X (n=35). Phenotypic resistance correlated with the AR genes identified in 95.4% of cases. Almost all AR genes were located on plasmids, with many of the plasmids encoding multiple AR genes. Thirteen AR genes representing five classes of antimicrobials were arranged into six highly conserved cassette-like sequences and one pseudo-cassette (1: sulII, strAB, tetAR; 2: aac3-iid; 3: aph, sph; 4: cmy-2; 5: floR; 6: tetB; pseudo: aadA, aac3-VIa, sulI). These cassettes were present in multiple isolates and on plasmids of multiple replicon types. To determine the current distribution and frequency of these cassettes, data in the public NCBI database was analyzed, including WGS data on isolates collected by the Food Safety and Inspection Service (FSIS) from 2014 to 2018. Cassettes one, four, and five were significantly associated with cattle while cassette six was significantly associated with chickens. This study reveals that a diverse group of plasmids carrying AR genes are responsible for the phenotypic resistance seen in Salmonella isolated from U.S. food animals. Many of these plasmids carry similar AR gene cassettes.