Potential risk-factors affecting Salmonella sp. and Escherichia coli occurrence and distribution in Midwestern United States swine feed mills

Graphical abstractGenotypic and Phenotypic Characterization of Antimicrobial and Heavy Metal tolerance in Salmonella enterica and Escherichia coli Isolates from Swine Feed Mills

Antimicrobials and heavy metals are commonly used in the animal feed industry. The role of in-feed antimicrobials on the evolution and persistence of resistance in enteric bacteria is not well described. Whole-Genome Sequencing (WGS) is widely used for genetic characterizations of bacterial isolates, including antimicrobial resistance, heavy metal tolerance, virulence factors, and relatedness to other sequenced isolates. The goals of this study were to i) use WGS to characterize Salmonella enterica (n = 33) and Escherichia coli (n = 30) isolated from swine feed and feed mill environments; and ii) investigate their genotypic and phenotypic antimicrobial and heavy metal tolerance. Salmonella isolates belonged to 10 serovars, the most common being Cubana, Senftenberg, and Tennessee. E. coli isolates were grouped into 22 O groups. Phenotypic resistance to at least one antimicrobial was observed in 19 Salmonella (57.6%) and 17 E. coli (56.7%) isolates, whereas multidrug resistance (resistant to ≥ 3 antimicrobial classes) was observed in four Salmonella (12%) and two E. coli (7%) isolates. Antimicrobial resistance genes were identified in 17 Salmonella (51%) and 29 E. coli (97%), with 11 and 29 isolates possessing genes conferring resistance to multiple antimicrobial classes. Phenotypically, 53% Salmonella and 58% E. coli presented resistance to copper and arsenic. All isolates that possessed the copper resistance operon were resistant to the highest concentration tested (40 mM). Heavy metal tolerance genes to copper and silver were present in 26 Salmonella isolates. Our study showed a strong agreement between predicted and measured resistances when comparing genotypic and phenotypic data for antimicrobial resistance, with an overall concordance of 99% and 98.3% for Salmonella and E. coli, respectively.

Salmonella detection in commercially prepared livestock feed and the raw ingredients and equipment used to manufacture the feed: A systematic review and meta-analysis

Salmonella contamination of livestock feed is a serious veterinary and public health issue. In this study we used a systematic review to assess the prevalence and characterization of Salmonella isolates detected in raw feed components, feed milling equipment and finished feed from 97 studies published from 1955 to 2020 across seven global regions. Eighty-five studies were included in a meta-analyses to estimate the combined prevalence of Salmonella detection and to compare the risk of contamination associated with different sample types. We found the overall combined prevalence estimate of Salmonella detection was 0.14 with a prevalence of 0.18 in raw feed components, 0.09 in finished feed and 0.08 in feed milling equipment. Animal based raw feed components were 3.9 times more likely to be contaminated with Salmonella than plant based raw feed components. Differences between studies accounted for 99 % of the variance in the prevalence estimate for all sample types and there was no effect of region on the prevalence estimates. The combined prevalence of Salmonella detection in raw feed components decreased from 0.25 in 1955 to 0.11 in 2019. The proportion of Salmonella isolates that were resistant to antimicrobials was largest for amikacin (0.20), tetracycline (0.18) streptomycin (0.17), cefotaxime (0.14) and sulfisoxazole (0.11). The prevalence of Salmonella contamination of animal feed varies widely between individual studies and is an ongoing challenge for the commercial feed industry. Control relies on the vigilant monitoring and control of Salmonella in each individual mill.