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.

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.

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.

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.

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.

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.

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.

Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring.

The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild-type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing, including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics, we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.

The mcr-9 Gene of Salmonella and Escherichia coli Is Not Associated with Colistin Resistance in the United States.

Reports of transmissible colistin resistance show the importance of comprehensive colistin resistance surveillance. Recently, a new allele of the mobile colistin resistance (mcr) gene family designated mcr-9, which shows variation in genetic context and colistin susceptibility, was reported. We tested over 100 Salmonella enterica and Escherichia coli isolates with mcr-9 from the National Antimicrobial Resistance Monitoring System (NARMS) in the United States for their susceptibility to colistin and found that every isolate was susceptible, with an MIC of ≤1 µg/ml. Long-read sequencing of 12 isolates revealed mcr-9 on IncHI plasmids that were either independent or integrated into the chromosome. Overall, these results demonstrate that caution is necessary when determining the clinical relevance of new resistance genes.

Photon skyshine from medical linear accelerators.

A widely used formula for the prediction of photon skyshine has been shown to be very inaccurate by comparison with numerous measurements. Discrepancies of up to an order of magnitude have been observed. In addition to this, the formula does not predict the observed dependence on field size, nor the fact that skyshine dose rates exhibit a local maximum. A scaling formula is derived here, with a single fitting parameter, which properly accounts for these properties, provides physical insight into the skyshine phenomenon, and is more accurate. The location of the maximum dose rate depends on the ratio of the roof height above isocenter to the distance from the isocenter to the outer surface of the sidewall. For nominal linac room dimensions, the maximum dose occurs at a distance from the outer wall of approximately two times the height of the roof above the isocenter. The skyshine dose rate is proportional to the field area and not Ω1.3 , as predicted by the standard formula, where Ω is the solid angle subtended by the beam. For lightly shielded roofs (concrete thickness less than about 0.5 m), the photon skyshine for 6 MV exceeds that for 18 MV. Evidence is presented that at intermediate distances the skyshine declines as one over the distance and not one over the distance squared. Predictions of skyshine dose rates depend critically on accurate knowledge of the roof transmission factor. If a roof is shielded so as to avoid designation as a "high radiation area," photon skyshine will be negligible.

Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States.

Increasingly, routine surveillance and monitoring of foodborne pathogens using whole-genome sequencing is creating opportunities to study foodborne illness epidemiology beyond routine outbreak investigations and case-control studies. Using a global phylogeny of Salmonella enterica serotype Typhimurium, we found that major livestock sources of the pathogen in the United States can be predicted through whole-genome sequencing data. Relatively steady rates of sequence divergence in livestock lineages enabled the inference of their recent origins. Elevated accumulation of lineage-specific pseudogenes after divergence from generalist populations and possible metabolic acclimation in a representative swine isolate indicates possible emergence of host adaptation. We developed and retrospectively applied a machine learning Random Forest classifier for genomic source prediction of Salmonella Typhimurium that correctly attributed 7 of 8 major zoonotic outbreaks in the United States during 1998-2013. We further identified 50 key genetic features that were sufficient for robust livestock source prediction.

Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates.

Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify AMR genes in whole-genome sequences, the National Center for Biotechnology Information (NCBI) has produced AMRFinder, a tool that identifies AMR genes using a high-quality curated AMR gene reference database. The Bacterial Antimicrobial Resistance Reference Gene Database consists of up-to-date gene nomenclature, a set of hidden Markov models (HMMs), and a curated protein family hierarchy. Currently, it contains 4,579 antimicrobial resistance proteins and more than 560 HMMs. Here, we describe AMRFinder and its associated database. To assess the predictive ability of AMRFinder, we measured the consistency between predicted AMR genotypes from AMRFinder and resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS). This included 5,425 Salmonella enterica, 770 Campylobacter spp., and 47 Escherichia coli isolates phenotypically tested against various antimicrobial agents. Of 87,679 susceptibility tests performed, 98.4% were consistent with predictions. To assess the accuracy of AMRFinder, we compared its gene symbol output with that of a 2017 version of ResFinder, another publicly available resistance gene detection system. Most gene calls were identical, but there were 1,229 gene symbol differences (8.8%) between them, with differences due to both algorithmic differences and database composition. AMRFinder missed 16 loci that ResFinder found, while ResFinder missed 216 loci that AMRFinder identified. Based on these results, AMRFinder appears to be a highly accurate AMR gene detection system.

Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella.

Nontyphoidal Salmonella species are the leading bacterial cause of foodborne disease in the United States. Whole-genome sequences and paired antimicrobial susceptibility data are available for Salmonella strains because of surveillance efforts from public health agencies. In this study, a collection of 5,278 nontyphoidal Salmonella genomes, collected over 15 years in the United States, was used to generate extreme gradient boosting (XGBoost)-based machine learning models for predicting MICs for 15 antibiotics. The MIC prediction models had an overall average accuracy of 95% within ±1 2-fold dilution step (confidence interval, 95% to 95%), an average very major error rate of 2.7% (confidence interval, 2.4% to 3.0%), and an average major error rate of 0.1% (confidence interval, 0.1% to 0.2%). The model predicted MICs with no a priori information about the underlying gene content or resistance phenotypes of the strains. By selecting diverse genomes for the training sets, we show that highly accurate MIC prediction models can be generated with less than 500 genomes. We also show that our approach for predicting MICs is stable over time, despite annual fluctuations in antimicrobial resistance gene content in the sampled genomes. Finally, using feature selection, we explore the important genomic regions identified by the models for predicting MICs. To date, this is one of the largest MIC modeling studies to be published. Our strategy for developing whole-genome sequence-based models for surveillance and clinical diagnostics can be readily applied to other important human pathogens.

Bayesian Recurrent Neural Network Models for Forecasting and Quantifying Uncertainty in Spatial-Temporal Data.

Recurrent neural networks (RNNs) are nonlinear dynamical models commonly used in the machine learning and dynamical systems literature to represent complex dynamical or sequential relationships between variables. Recently, as deep learning models have become more common, RNNs have been used to forecast increasingly complicated systems. Dynamical spatio-temporal processes represent a class of complex systems that can potentially benefit from these types of models. Although the RNN literature is expansive and highly developed, uncertainty quantification is often ignored. Even when considered, the uncertainty is generally quantified without the use of a rigorous framework, such as a fully Bayesian setting. Here we attempt to quantify uncertainty in a more formal framework while maintaining the forecast accuracy that makes these models appealing, by presenting a Bayesian RNN model for nonlinear spatio-temporal forecasting. Additionally, we make simple modifications to the basic RNN to help accommodate the unique nature of nonlinear spatio-temporal data. The proposed model is applied to a Lorenz simulation and two real-world nonlinear spatio-temporal forecasting applications.

Identification and Characterization of Conjugative Plasmids That Encode Ciprofloxacin Resistance in Salmonella.

This study aimed to characterize novel conjugative plasmids that encode transferable ciprofloxacin resistance in Salmonella In this study, 157 nonduplicated Salmonella isolates were recovered from food products, of which 55 were found to be resistant to ciprofloxacin. Interestingly, 37 of the 55 CiprSalmonella isolates (67%) did not harbor any mutations in the quinolone resistance-determining regions (QRDR). Six Salmonella isolates were shown to carry two novel types of conjugative plasmids that could transfer the ciprofloxacin resistance phenotype to Escherichia coli J53 (azithromycin resistant [Azir]). The first type of conjugative plasmid belonged to the ∼110-kb IncFIB-type conjugative plasmids carrying qnrB-bearing and aac(6')-Ib-cr-bearing mobile elements. Transfer of the plasmid between E. coli and Salmonella could confer a ciprofloxacin MIC of 1 to 2 µg/ml. The second type of conjugative plasmid belonged to ∼240-kb IncH1/IncF plasmids carrying a single PMQR gene, qnrS Importantly, this type of conjugative ciprofloxacin resistance plasmid could be detected in clinical Salmonella isolates. The dissemination of these conjugative plasmids that confer ciprofloxacin resistance poses serious challenges to public health and Salmonella infection control.

Novel linezolid resistance plasmids in Enterococcus from food animals in the USA.

Objectives: To sequence the genomes and determine the genetic mechanisms for linezolid resistance identified in three strains of Enterococcus isolated from cattle and swine caecal contents as part of the US National Antimicrobial Resistance Monitoring System (NARMS) surveillance programme. Methods: Broth microdilution was used for in vitro antimicrobial susceptibility testing to assess linezolid resistance. Resistance mechanisms and plasmid types were identified from data generated by WGS on Illumina® and PacBio® platforms. Conjugation experiments were performed to determine whether identified mechanisms were transmissible. Results: Linezolid resistance plasmids containing optrA were identified in two Enterococcus faecalis isolates and one Enterococcus faecium. The E. faecium isolate also carried the linezolid resistance gene cfr on the same plasmid as optrA. The linezolid resistance plasmids had various combinations of additional resistance genes conferring resistance to phenicols (fexA), aminoglycosides [spc and aph(3')-III] and macrolides [erm(A) and erm(B)]. One of the plasmids was confirmed to be transmissible by conjugation, resulting in linezolid resistance in the transconjugant. Conclusions: To the best of our knowledge, this is the first identification of linezolid resistance in the USA in bacteria isolated from food animals. The oxazolidinone class of antibiotics is not used in food animals in the USA, but the genes responsible for resistance were identified on plasmids with other resistance markers, indicating that there may be co-selection for these plasmids due to the use of different antimicrobials. The transmissibility of one of the plasmids demonstrated the potential for linezolid resistance to spread horizontally. Additional surveillance is necessary to determine whether similar plasmids are present in human strains of Enterococcus.

Prevalence and Antimicrobial Resistance of Enterococci Isolated from Retail Meats in the United States, 2002 to 2014.

Bacteria of the genus Enterococcus are important human pathogens that are frequently resistant to a number of clinically important antibiotics. They are also used as markers of animal fecal contamination of human foods and are employed as sentinel organisms for tracking trends in resistance to antimicrobials with Gram-positive activity. As part of the National Antimicrobial Resistance Monitoring System (NARMS), we evaluated several retail meat commodities for the presence of enterococci from 2002 to 2014, and we found 92.0% to be contaminated. The majority of isolates were either Enterococcus faecalis (64.0%) or Enterococcus faecium (28.6%), and the antimicrobial resistance of each isolate was assessed by broth microdilution. The resistance prevalences for several drugs, including erythromycin and gentamicin, were significantly higher among poultry isolates, compared to retail beef or pork isolates. None of the isolates was resistant to the clinically important human drug vancomycin, only 1 isolate was resistant to linezolid, and resistance to tigecycline was below 1%. In contrast, a majority of both E. faecalis (67.5%) and E. faecium (53.7%) isolates were resistant to tetracycline. Overall, the robust NARMS testing system employed consistent sampling practices and methods throughout the testing period, with the only significant trend in resistance prevalence being decreased E. faecium resistance to penicillin. These data provide excellent baseline levels of resistance that can be used to measure future changes in resistance prevalence that may result from alterations in the use of antimicrobials in food animal production.IMPORTANCE Enterococci, including E. faecalis and E. faecium, are present in the guts of food-producing animals and are used as a measure of fecal contamination of meat. We used the large consistent sampling methods of NARMS to assess the prevalence of Enterococcus strains isolated from retail meats, and we found over 90% of meats to be contaminated with enterococci. We also assessed the resistance of the Enterococcus strains, commonly used as a measure of resistance to agents with Gram-positive activity, in foods. Resistance prevalence was over 25% for some antimicrobials and sample sources but was less than 1% for several of the most important therapeutic agents used in human medicine.

Sequence Analysis of IncA/C and IncI1 Plasmids Isolated from Multidrug-Resistant Salmonella Newport Using Single-Molecule Real-Time Sequencing.

Multidrug-resistant (MDR) plasmids play an important role in disseminating antimicrobial resistance genes. To elucidate the antimicrobial resistance gene compositions in A/C incompatibility complex (IncA/C) plasmids carried by animal-derived MDR Salmonella Newport, and to investigate the spread mechanism of IncA/C plasmids, this study characterizes the complete nucleotide sequences of IncA/C plasmids by comparative analysis. Complete nucleotide sequencing of plasmids and chromosomes of six MDR Salmonella Newport strains was performed using PacBio RSII. Open reading frames were assigned using prokaryotic genome annotation pipeline (PGAP). To understand genomic diversity and evolutionary relationships among Salmonella Newport IncA/C plasmids, we included three complete IncA/C plasmid sequences with similar backbones from Salmonella Newport and Escherichia coli: pSN254, pAM04528, and peH4H, and additional 200 draft chromosomes. With the exception of canine isolate CVM22462, which contained an additional IncI1 plasmid, each of the six MDR Salmonella Newport strains contained only the IncA/C plasmid. These IncA/C plasmids (including references) ranged in size from 80.1 (pCVM21538) to 176.5 kb (pSN254) and carried various resistance genes. Resistance genes floR, tetA, tetR, strA, strB, sul, and mer were identified in all IncA/C plasmids. Additionally, blaCMY-2 and sugE were present in all IncA/C plasmids, excepting pCVM21538. Plasmid pCVM22462 was capable of being transferred by conjugation. The IncI1 plasmid pCVM22462b in CVM22462 carried blaCMY-2 and sugE. Our data showed that MDR Salmonella Newport strains carrying similar IncA/C plasmids clustered together in the phylogenetic tree using chromosome sequences and the IncA/C plasmids from animal-derived Salmonella Newport contained diverse resistance genes. In the current study, we analyzed genomic diversities and phylogenetic relationships among MDR Salmonella Newport using complete plasmids and chromosome sequences and provided possible spread mechanism of IncA/C plasmids in Salmonella Newport Lineage II.

Identification of Plasmid-Mediated Quinolone Resistance in Salmonella Isolated from Swine Ceca and Retail Pork Chops in the United States.

Fluoroquinolones are important antimicrobial drugs used to treat human Salmonella infections, and resistance is rare in the United States for isolates from human and animal sources. Recently, a number of Salmonella isolates from swine cecal contents and retail pork products from National Antimicrobial Resistance Monitoring System (NARMS) surveillance exhibited decreased susceptibility to ciprofloxacin. We identified two qnrB19 quinolone resistance plasmids that are predominantly responsible for this phenomenon and found them distributed among several Salmonella serotypes isolated throughout the United States.