Rapid Screening for Salmonella in Raw Pet Food by Loop-Mediated Isothermal Amplification

Genomic analysis of azithromycin-resistant Salmonella from food animals at slaughter and processing, and retail meats, 2011-2021, United States

IMPORTANCE

Macrolides of different ring sizes are critically important antimicrobials for human medicine and veterinary medicine, though the widely used 15-membered ring azithromycin in humans is not approved for use in veterinary medicine. We document here the emergence of azithromycin-resistant Salmonella among the NARMS culture collections between 2011 and 2021 in food animals and retail meats, some with co-resistance to ceftriaxone or decreased susceptibility to ciprofloxacin. We also provide insights into the underlying genetic mechanisms and genomic contexts, including the first report of a novel combination of azithromycin resistance determinants and the characterization of multidrug-resistant plasmids. Further, we highlight the emergence of a multidrug-resistant Salmonella Newport clone in food animals (mainly cattle) with both azithromycin resistance and decreased susceptibility to ciprofloxacin. These findings contribute to a better understating of azithromycin resistance mechanisms in Salmonella and warrant further investigations on the drivers behind the emergence of resistant clones.

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.

Application of encapsulated and dry-plated food acidulants to control Salmonella enterica in raw meat-based diets for dogs

There is an increasing demand for raw meat-based diets (RMBDs) for dogs, but these foods cannot be heat-pasteurized. Thus, the objective of this study was to evaluate the antimicrobial efficacy of encapsulated and dry-plated glucono delta lactone (GDL), citric acid (CA), and lactic acid (LA) when challenged against Salmonella enterica inoculated in a model raw meat-based diet (RMBDs) for dogs. Nutritionally complete, raw diets were formulated with different levels (1.0, 2.0 and 3.0% (w/w)) of both encapsulated and dry-plated GDL, CA, and LA with both the positive (PC) and the negative controls (NC) without acidulants. The diets were formed into patties of ∼100 g and inoculated with 3-cocktail mixtures of Salmonella enterica serovars, excluding the NC to achieve a final concentration of ∼6.0 Log CFU/patty. Microbial analyses were performed on the inoculated diets and survivors of S. enterica enumerated. Both encapsulated and dry-plated CA and LA had higher log reductions compared to GDL (P < 0.05). However, encapsulated CA and LA at 1.0% (w/w) exhibited higher log reductions (P > 0.05) and preserved product quality compared to the dry-plated acidulants at 1.0%. We concluded that 1.0% (w/w) of encapsulated citric or lactic acids could be successfully applied as an antimicrobial intervention in raw diets for dogs.

Toward the Adoption of Loop-Mediated Isothermal Amplification for Salmonella Screening at the National Antimicrobial Resistance Monitoring System's Retail Meat Sites

The National Antimicrobial Resistance Monitoring System (NARMS) is a One Health program in the United States that collects data on antimicrobial resistance in enteric bacteria from humans, animals, and the environment. Salmonella is a major pathogen tracked by the NARMS retail meat arm but currently lacks a uniform screening method. We evaluated a loop-mediated isothermal amplification (LAMP) assay for the rapid screening of Salmonella from 69 NARMS retail meat and poultry samples. All samples were processed side by side for culture isolation using two protocols, one from NARMS and the other one described in the U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM). Overall, 10 (14.5%) samples screened positive by the Salmonella LAMP assay. Of those, six were culture-confirmed by the NARMS protocol and six by the BAM method with overlap on four samples. No Salmonella isolates were recovered from samples that screened negative with LAMP. These results suggested 100% sensitivity for LAMP in reference to culture. Antimicrobial susceptibility testing and whole-genome sequencing analysis confirmed identities of these isolates. Using the BAM protocol, all Salmonella isolates were recovered from samples undergoing Rappaport-Vassiliadis medium selective enrichment and presumptive colonies (n = 130) were dominated by Hafnia alvei (44.6%), Proteus mirabilis (22.3%), and Morganella morganii (9.9%) based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This method comparison study clearly demonstrated the benefit of a rapid, robust, and highly sensitive molecular screening method in streamlining the laboratory workflow. Fourteen NARMS retail meat sites further verified the performance of this assay using a portion of their routine samples, reporting an overall specificity of 98.8% and sensitivity of 90%. As of July 2022, the vast majority of NARMS retail meat sites have adopted the Salmonella LAMP assay for rapid screening of Salmonella in all samples.

Versatility of a Salmonella Loop-Mediated Isothermal Amplification Assay Using Multiple Platforms and Master Mixes in Animal Food Matrices

Background

Improvement in Salmonella detection methods greatly enhances the efficiency of various food testing programs. A Salmonella loop-mediated isothermal amplification (LAMP) assay has been validated in animal food through multi-laboratory validation.

Objective

The study aimed to demonstrate the versatility of this molecular assay while expanding it to multiple platforms and various reagent choices for use in animal food testing.

Methods

Following the U.S. Food and Drug Administration (FDA)’s Guidelines for the Validation of Analytical Methods for the Detection of Microbial Pathogens in Foods and Feeds, we examined the inclusivity, exclusivity, and LOD of the assay using two platforms (7500 Fast and Genie II) and three LAMP master mixes (GspSSD, GspSSD2.0, and WarmStart) in seven animal food matrixes (dry cat food, dry dog food, cattle feed, dairy feed, horse feed, poultry feed, and swine feed). The FDA’s Bacteriological Analytical Manual (BAM) Salmonella culture method was the reference method.

Results

Inclusivity and exclusivity data were consistent among all six platform and master mix combinations with a few exceptions. Comparable LODs were observed down to the single-cell level (WarmStart was 10-fold less sensitive). Performance was similar to the BAM method for detecting fractional positive results in seven animal food matrixes. Nonetheless, LAMP time to positive results and annealing/melting temperature differed among master mixes and platforms.

Conclusion

The Salmonella LAMP assay was successfully validated in two platforms and three master mixes, making it a flexible tool for use by the FDA’s field laboratories in regulatory testing of animal food and for adoption by other food testing programs.

Highlights

We demonstrated the LAMP assay’s versatility on two platforms and three master mixes for the rapid and reliable screening of Salmonella in seven animal food matrixes. GspSSD2.0 was the fastest master mix (time to positive results as early as 3.5 min) while Genie II had several attractive features from a user perspective.

Microbiological Hazards in Dry Dog Chews and Feeds

Nowadays, dogs are usually equally treated with other family members. Due to the growing caregivers' awareness, the pet foods industry is changing dynamically. Pet foods are manufactured with a myriad of ingredients. Few authors of scientific papers deal with the topic of foods products' safety for pet animals, assessed from the perspective of their caregivers. Despite the many methods of producing foods of the highest quality, there are still cases of contamination of pet foods and treats. In the case of dried chews for dogs, bacteria of the genus Salmonella are the most common risk. In the case of both dry and wet foods, in addition to many species of bacteria, we often deal with mold fungi and their metabolites, mycotoxins. This article presents selected microbiological risks in dog foods and treats, and analyzes the Rapid Alert System for Food and Feed (RASFF) system (2017-2020) for pathogenic microorganisms in dried dog chews, treats and foods. In this period, pet food-related notifications were registered, which were categorized into different types. Analyzing the RASFF notifications over the period, it has been shown that there are still cases of bacterial contamination of dog foods and treats, while in terms of the overall mycotoxin content, these products may appear safe.