A one health approach for monitoring antimicrobial resistance: developing a national freshwater pilot effort.

Antimicrobial resistance (AMR) is a world-wide public health threat that is projected to lead to 10 million annual deaths globally by 2050. The AMR public health issue has led to the development of action plans to combat AMR, including improved antimicrobial stewardship, development of new antimicrobials, and advanced monitoring. The National Antimicrobial Resistance Monitoring System (NARMS) led by the United States (U.S) Food and Drug Administration along with the U.S. Centers for Disease Control and U.S. Department of Agriculture has monitored antimicrobial resistant bacteria in retail meats, humans, and food animals since the mid 1990's. NARMS is currently exploring an integrated One Health monitoring model recognizing that human, animal, plant, and environmental systems are linked to public health. Since 2020, the U.S. Environmental Protection Agency has led an interagency NARMS environmental working group (EWG) to implement a surface water AMR monitoring program (SWAM) at watershed and national scales. The NARMS EWG divided the development of the environmental monitoring effort into five areas: (i) defining objectives and questions, (ii) designing study/sampling design, (iii) selecting AMR indicators, (iv) establishing analytical methods, and (v) developing data management/analytics/metadata plans. For each of these areas, the consensus among the scientific community and literature was reviewed and carefully considered prior to the development of this environmental monitoring program. The data produced from the SWAM effort will help develop robust surface water monitoring programs with the goal of assessing public health risks associated with AMR pathogens in surface water (e.g., recreational water exposures), provide a comprehensive picture of how resistant strains are related spatially and temporally within a watershed, and help assess how anthropogenic drivers and intervention strategies impact the transmission of AMR within human, animal, and environmental systems.

Paired metagenomic and chemical evaluation of aflatoxin-contaminated dog kibble.

Introduction: Identification of chemical toxins from complex or highly processed foods can present 'needle in the haystack' challenges for chemists. Metagenomic data can be used to guide chemical toxicity evaluations by providing DNA-based description of the wholistic composition (eukaryotic, bacterial, protozoal, viral, and antimicrobial resistance) of foods suspected to harbor toxins, allergens, or pathogens. This type of information can focus chemistry-based diagnostics, improve hazard characterization and risk assessment, and address data gaps. Additionally, there is increasing recognition that simultaneously co-occurring mycotoxins, either from single or multiple species, can impact dietary toxicity exposure. Metagenomic data provides a way to address data gaps related to co-occurrence of multiple fungal species. Methods: Paired metagenomic and chemical data were used to evaluate aflatoxin-contaminated kibble with known levels of specific mycotoxins. Kibble was ground to a fine powder for both chemical and molecular analyses. Chemical analyses were performed with Liquid Chromatography Mass Spectrometry (LCMS) and according to the AOAC Official method 2005.08: Aflatoxins in Corn, Raw Peanuts, and Peanut Butter using Liquid Chromatography with Post-Column Photochemical Derivatization. Metagenomes were created from DNA extracted from ground kibble and sequenced on an Illumina NextSeq 2000 with an average sequence depth of 180 million reads per replicate. Results and discussion: Metagenomic data demonstrated that the abundance of DNA from putative aflatoxigenic Aspergillus spp. correlated with the levels of aflatoxin quantified by LCMS. Metagenomic data also identified an expansive range of co-occurring fungal taxa which may produce additional mycotoxins. DNA data paired with chemical data provides a novel modality to address current data gaps surrounding dietary mycotoxin exposure, toxigenic fungal taxonomy, and mycotoxins of emerging concern.

Monte Carlo evaluation of uncertainties in photon and electron TG-51 absorbed dose calibration.

PURPOSE: The accuracy of dose delivery to all patients treated with medical linacs depends on the accuracy of beam calibration. Dose delivery cannot be any more accurate than this. Given the importance of this, it seems worthwhile taking another look at the expected uncertainty in TG-51 photon dose calibration and a first look at electron calibration. This work builds on the 2014 addendum to TG-51 for photons and adds to it by also considering electrons. In that publication, estimates were made of the uncertainty in the dose calibration. In this paper, we take a deeper look at this important issue. METHODS: The methodology used here is more rigorous than previous determinations as it is based on Monte Carlo simulation of uncertainties. It is assumed that mechanical QA has been performed following TG-142 prior to beam calibration and that there are no uncertainties that exceed the tolerances specified by TG-142. RESULTS/CONCLUSIONS: Despite the different methodology and assumptions, the estimated uncertainty in photon beam calibration is close to that in the addendum. The careful user should be able to easily reach a 95% confidence interval (CI) of ± 2.3% for photon beam calibration with standard instrumentation. For electron beams calibrated with a Farmer chamber, the estimated uncertainties are slightly larger, and the 95% CI is ±2.6% for 6 MeV and slightly smaller than this for 18 MeV. There is no clear energy dependence in these results. It is unlikely that the user will be able to improve on these uncertainties as the dominant factor in the uncertainty resides in the ion chamber dose calibration factor N D , w 60 Co $N_{D,w}^{{}^{60}{\mathrm{Co}}}$ . For both photons and electrons, reduction in the ion chamber depth uncertainty below about 0.5 mm and SSD uncertainty below 1 mm have almost no effect on the total dose uncertainty, as uncertainties beyond the user's control totally dominate under these circumstances.

The spread of pESI-mediated extended-spectrum cephalosporin resistance in Salmonella serovars-Infantis, Senftenberg, and Alachua isolated from food animal sources in the United States.

The goal of this study is to investigate the origin, prevalence, and evolution of the pESI megaplasmid in Salmonella isolated from animals, foods, and humans. We queried 510,097 Salmonella genomes under the National Center for Biotechnology Information (NCBI) Pathogen Detection (PD) database for the presence of potential sequences containing the pESI plasmid in animal, food, and environmental sources. The presence of the pESI megaplasmid was confirmed by using seven plasmid-specific markers (rdA, pilL, SogS, TrbA, ipf, ipr2 and IncFIB(pN55391)). The plasmid and chromosome phylogeny of these isolates was inferred from single nucleotide polymorphisms (SNPs). Our search resolved six Salmonella clusters carrying the pESI plasmid. Four were emergent Salmonella Infantis clusters, and one each belonged to serovar Senftenberg and Alachua. The Infantis cluster with a pESI plasmid carrying blaCTX-M-65 gene was the biggest of the four emergent Infantis clusters, with over 10,000 isolates. This cluster was first detected in South America and has since spread widely in United States. Over time the composition of pESI in United States has changed with the average number of resistance genes showing a decrease from 9 in 2014 to 5 in 2022, resulting from changes in gene content in two integrons present in the plasmid. A recent and emerging cluster of Senftenberg, which carries the blaCTX-M-65 gene and is primarily associated with turkey sources, was the second largest in the United States. SNP analysis showed that this cluster likely originated in North Carolina with the recent acquisition of the pESI plasmid. A single Alachua isolate from turkey was also found to carry the pESI plasmid containing blaCTX-M-65 gene. The study of the pESI plasmid, its evolution and mechanism of spread can help us in developing appropriate strategies for the prevention and further spread of this multi-drug resistant plasmid in Salmonella in poultry and humans.

Internal lead shielding for clinical electron treatments.

Electron beams are often used to treat superficial lesions of the lip, cheek, nose, and ear. Lead is frequently used to block distal structures. It is customary to place an internal bolus of low atomic number in between the tissue and the lead to reduce electron backscatter from the lead. Space for the lead and the internal bolus is quite limited. A previous method for estimating the thickness of the lead plus internal bolus is not self-consistent and leads to a larger than necessary thickness. A new method is described here to provide a quick, accurate, and self-consistent estimate of the minimum necessary thickness of the internal bolus and the lead for incident electron beam energies of 4, 6, 8, 9, and 10 MeV as a function of the thickness of the overlying tissue. This method limits the dose enhancement at the tissue/bolus interface due to the underlying lead to 10%. Measurements made with gafchromic film validate this methodology.

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.

Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting.

Here, we describe the fecal microbiome of laboratory beagles in a non-invasive experiment designed to contrast in vivo versus in vitro bioequivalence in response to antiparasitic drug administration. The experiment provided a unique opportunity to evaluate metagenomic profiles of canine feces before and after anti-parasitic drug exposure.

Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact.

Here, we examine surface waters as a modality to better understand baseline antimicrobial resistance (AMR) across the environment to supplement existing AMR monitoring in pathogens associated with humans, foods, and animals. Data from metagenomic and quasimetagenomic (shotgun sequenced enrichments) are used to describe AMR in Maryland surface waters from high and low human impact classifications.

A comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories.

Developing effective and sensitive detection methods for antimicrobial resistant Salmonella enterica from surface water is a goal of the National Antimicrobial Resistance Monitoring System (NARMS). There are no specified methods for recovery of S. enterica in surface waters in the U.S. A multi-laboratory evaluation of four methods - bulk water enrichment (BW), vertical Modified Moore Swab (VMMS), modified Standard Method 9260.B2 (SM), and dead-end ultrafiltration (DEUF) - was undertaken to recover S. enterica from surface water. In Phase 1, one-liter volumes of water were collected from the same site on five different dates. Water was shipped and analyzed at four different laboratory locations (A, B, C, and D) for recovery of 1) inoculated fluorescent S. Typhimurium strain (ca. 30 CFU/L) and 2) Salmonella present in the water sampled. At each location, BW, VMMS, or SM recovery was performed on five separate 1 L water samples. Twenty 1 L water samples were subjected to each recovery method, and overall, sixty 1 L samples were assayed for Salmonella. Inoculated, fluorescent Salmonella Typhimurium and environmental Salmonella spp. were recovered from 65 % (39/60) and 45 % (27/60) of water samples, respectively. BW, VMMS, and SM recovered fluorescent S. Typhimurium from 60 %, 60 %, and 75 % of inoculated samples, respectively. Analysis by Chi-squared test determined laboratory location had a significant (p < 0.05) effect on fluorescent S. Typhimurium recovery compared to method or date of water collection. In Phase 2, recovery of inoculated fluorescent S. Typhimurium from 1 L samples by SM and DEUF was compared at laboratory locations B and D. SM and DEUF recovered fluorescent S. Typhimurium from 100 % (20/20) and 95 % (19/20) of inoculated water samples, respectively; laboratory location (p > 0.05) did not affect Salmonella recovery. Uniform laboratory methodology and training should be prioritized in conducting Salmonella recovery from surface water in laboratories.

Lociq provides a loci-seeking approach for enhanced plasmid subtyping and structural characterization.

Antimicrobial resistance (AMR) monitoring for public health is relying more on whole genome sequencing to characterize and compare resistant strains. This requires new approaches to describe and track AMR that take full advantage of the detailed data provided by genomic technologies. The plasmid-mediated transfer of AMR genes is a primary concern for AMR monitoring because plasmid rearrangement events can integrate new AMR genes into the plasmid backbone or promote hybridization of multiple plasmids. To better monitor plasmid evolution and dissemination, we developed the Lociq subtyping method to classify plasmids by variations in the sequence and arrangement of core plasmid genetic elements. Subtyping with Lociq provides an alpha-numeric nomenclature that can be used to denominate plasmid population diversity and characterize the relevant features of individual plasmids. Here we demonstrate how Lociq generates typing schema to track and characterize the origin, evolution and epidemiology of multidrug resistant plasmids.

Linac primary barrier transmission: Flattening filter free and field size dependence.

There is widespread consensus in the literature that flattening filter free (FFF) beams have a lower primary barrier transmission than flattened beams. Measurements presented here, however, show that for energy compensated FFF beams, the barrier transmission can be as much as 70% higher than for flattened beams. The ratio of the FFF barrier transmission to the flattened beam barrier transmission increases with increasing barrier thickness. The use of published FFF TVL data for energy compensated FFF beams could lead to an order of magnitude underestimate of the air kerma rate. There are little data in the literature on the field size dependence of the barrier transmission for flattened beams. Barrier transmission depends on the field size at the barrier, not at isocenter Measurements are presented showing the relative dependence of barrier transmission on the field size, measured at the barrier, for 6 MV and 10 MV beams. An analytical fitting formula is provided for the field size dependence. For field sizes greater than about 150 cm in side length, the field size dependence is minimal. For field sizes less than about 100 cm, the transmission declines rapidly as the field size decreases.

Geography shapes the genomics and antimicrobial resistance of Salmonella enterica Serovar Enteritidis isolated from humans.

Multidrug-resistant (MDR) Salmonella has been a long-standing challenge in public health and food safety. The prevalence of MDR S. Enteritidis, especially isolated from humans, in China is significantly higher than those from the U.S. and other countries. A dataset of 197 S. Enteritidis genomes, including 16 sequenced clinical isolates from China and 181 downloaded genomes of human isolates from the U.S., Europe, and Africa, was analyzed for genomic diversity, virulence potential, and antimicrobial resistance (AMR). Phylogenomic analyses identified four major well-supported clades (I-IV). While AMR genotype in the majority of isolates in clades I and IV displayed as pan-susceptible, 81.8% (9/11) and 22.4% (13/58) of isolates in clades III and II were MDR, respectively. It is noted that 77% (10/13) of MDR isolates in clade II were from China. The most common antimicrobial resistance genes (ARGs) carried by the Chinese isolates were aph(3')-IIa, blaCTX-M-55, and blaTEM-1B, whereas blaTEM-1B, sul1, sul2, drfA7, aph(3")-Ib/strA, and aph(6)-Id/strB were most often identified in those from Africa (clade III). Among the 14 plasmid types identified, IncX1 and IncFII(pHN7A8) were found exclusively in the Chinese MDR isolates, while IncQ1 was highly associated with the African MDR isolates. The spvRABCD virulence operon was present in 94.9% (187/197) of isolates tested and was highly associated with both the IncF (IncFII and IncFIB) plasmids. In addition, phylogenetic differences in distribution of Salmonella pathogenicity islands (SPIs), prophages and other accessory genes were also noted. Taken together, these findings provide new insights into the molecular mechanisms underpinning diversification of MDR S. Enteritidis.

Linac primary barrier transmission for concrete: Monte Carlo calculations.

Recent publications have called into question the accuracy of reference tenth-value layer (TVL) data cited in official reports for linac primary concrete barriers. Doubts have arisen based on both experimental and theoretical evidence. Most of the standard reference TVL values trace back to a publication that appeared in 1984 that used beam spectra that are not representative of modern linacs. This study reports a new set of TVL data for concrete based on modern linac beam spectra and a definition of the barrier transmission that is consistent with its use in shielding calculations. TVL values have been computed for concrete using Monte Carlo simulation for beam energies of 4, 6, 10, 15, and 18 MV. The barrier transmission depends on the field size at the barrier and the distance from the distal surface of the barrier to the point of observation. The TVL values reported here lead to barrier transmission values that are up to a factor of 4 larger than those in official reports. The air kerma rate beyond the barrier does not obey an inverse square law as the barrier now acts like a new (non-point) source of radiation. For distance greater than 0.3 m from the distal side of the barrier, inverse square predictions of the air kerma rate are low by up to a factor of 2. The average energy of the transmitted photons declines rapidly for all beam energies with increasing barrier thickness up to a thickness of about 50 cm and then slowly increases with increasing thickness.

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.

Prevalence of Antimicrobial Resistance in Select Bacteria From Retail Seafood-United States, 2019.

In 2019, the United States National Antimicrobial Resistance Monitoring System (NARMS) surveyed raw salmon, shrimp, and tilapia from retail grocery outlets in eight states to assess the prevalence of bacterial contamination and antimicrobial resistance (AMR) in the isolates. Prevalence of the targeted bacterial genera ranged among the commodities: Salmonella (0%-0.4%), Aeromonas (19%-26%), Vibrio (7%-43%), Pseudomonas aeruginosa (0.8%-2.3%), Staphylococcus (23%-30%), and Enterococcus (39%-66%). Shrimp had the highest odds (OR: 2.8, CI: 2.0-3.9) of being contaminated with at least one species of these bacteria, as were seafood sourced from Asia vs. North America (OR: 2.7; CI: 1.8-4.7) and Latin America and the Caribbean vs. North America (OR: 1.6; CI: 1.1-2.3) and seafood sold at the counter vs. sold frozen (OR: 2.1; CI: 1.6-2.9). Isolates exhibited pan-susceptibility (Salmonella and P. aeruginosa) or low prevalence of resistance (<10%) to most antimicrobials tested, with few exceptions. Seafood marketed as farm-raised had lower odds of contamination with antimicrobial resistant bacteria compared to wild-caught seafood (OR: 0.4, CI: 0.2-0.7). Antimicrobial resistance genes (ARGs) were detected for various classes of medically important antimicrobials. Clinically relevant ARGs included carbapenemases (bla IMI-2, bla NDM-1) and extended spectrum ß-lactamases (ESBLs; bla CTX-M-55). This population-scale study of AMR in seafood sold in the United States provided the basis for NARMS seafood monitoring, which began in 2020.

Uncertainties in linac primary barrier transmission values.

Primary barrier design for linac shielding depends very sensitively on tenth value layer (TVL) data. Inaccuracies can lead to large discrepancies between measured and calculated values of the barrier transmission. Values of the TVL for concrete quoted in several widely used standard references are substantially different than those calculated more recently. The older standard TVL data predict significantly lower radiation levels outside primary barriers than the more recently calculated values under some circumstances. The difference increases with increasing barrier thickness and energy, and it can be as large as a factor of 4 for 18 MV and concrete thickness of 200 cm. This may be due to significant differences in the beam spectra between the earlier and the more recent calculations. Measured instantaneous air kerma rates sometimes show large variations for the same energy and thickness. This may be due to confounding factors such as extra material on, or inside the barrier, variable field size at the barrier, density of concrete, and distal distance from the barrier surface. In some cases, the older TVL data significantly underestimate measured instantaneous air kerma rates, by up to a factor of 3, even when confounding factors are taken into account. This could lead to the necessity for expensive remediation. The more recent TVL values tend to overestimate the measured instantaneous dose rates. Reference TVL data should be computed in a manner that is mathematically consistent with their use in the calculation of air kerma rate outside barriers directly from the linac "dose" rate in MU/min.

Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States.

ABSTRACT: This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety.

Medical linac photon skyshine: Monte Carlo calculations and a methodology for estimates.

It has been shown that a widely quoted formula for estimating medical linac photon skyshine equivalent doses is erroneous. Monte Carlo calculations have been performed to develop an easy method for quickly and accurately estimating skyshine radiation levels and to gain improved physical insight into the skyshine phenomenon. Calculations of linac photon skyshine have been performed for 4, 6, 10, 15, and 18 MV beams for 10 × 10 cm2 and 40 × 40 cm2 fields and for a range of room dimensions and roof thicknesses. The effect of flattening filter free beams has been considered. Air kerma rates (AKRs) can be accurately fitted to a simple algebraic formula that is a function of the horizontal distance from the isocenter with a single energy dependent fitting parameter. The AKR, at a height of 1.3 m above level ground, reaches a local maximum at a distance dmax  = 1.5dw + 1.1h, where dw is the horizontal distance from the isocenter to the outside of the side wall, and h is the vertical distance from the isocenter to the top of the roof. For thin roofs, low energy beams lead to significantly more skyshine than high energy beams because low energy photons are more easily scattered through large angles. In the absence of a roof, the maximum skyshine dose rate is on the order of 8 × 10-7 times the dose rate at isocenter. The average energy of the skyshine photons is about 0.15 MeV, and it is remarkably independent of almost all parameters. A simple methodology is outlined for the evaluation of photon skyshine.

Long-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in Salmonella enterica.

Salmonella enterica is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on Salmonella isolated from retail meats and food animals. A collection of 134 multidrug-resistant isolates belonging to 33 serotypes were subjected to PacBio sequencing. One major locus of diversity among these isolates was the presence and orientation of Salmonella pathogenic islands (SPI), which varied across different serotypes but were largely conserved within individual serotypes. We also identified insertion of an IncQ resistance plasmid into the chromosome of fourteen strains of serotype I 4,[5],12:i:- and the Salmonella genomic island 1 (SGI-1) in five serotypes. The presence of various SPIs, SGI-1 and integrated plasmids contributed significantly to the genomic variability and resulted in chromosomal resistance in 55.2% (74/134) of the study isolates. A total of 93.3% (125/134) of isolates carried at least one plasmid, with isolates carrying up to seven plasmids. We closed 233 plasmid sequences of thirteen replicon types, along with twelve hybrid plasmids. Some associations between Salmonella isolate source, serotype, and plasmid type were seen. For instance, IncX plasmids were more common in serotype Kentucky from retail chicken. Plasmids IncC and IncHI had on average more than five antimicrobial resistance genes, whereas in IncX, it was less than one per plasmid. Overall, 60% of multidrug resistance (MDR) strains that carried >3 AMR genes also carried >3 heavy metal resistance genes, raising the possibility of co-selection of antimicrobial resistance in the presence of heavy metals. We also found nine isolates representing four serotypes that carried virulence plasmids with the spv operon. Together, these data demonstrate the power of long-read sequencing to reveal genomic arrangements and integrated plasmids with a high level of resolution for tracking and comparing resistant strains from different sources. Additionally, the findings from this study will help expand the reference set of closed Salmonella genomes that can be used to improve genome assembly from short-read data commonly used in One Health antimicrobial resistance surveillance.