Exact Universal Bounds on Quantum Dynamics and Fast Scrambling.

Quantum speed limits such as the Mandelstam-Tamm or Margolus-Levitin bounds offer a quantitative formulation of the energy-time uncertainty principle that constrains dynamics over short times. We show that the spectral form factor, a central quantity in quantum chaos, sets a universal state-independent bound on the quantum dynamics of a complete set of initial states over arbitrarily long times, which is tighter than the corresponding state-independent bounds set by known speed limits. This bound further generalizes naturally to the real-time dynamics of time-dependent or dissipative systems where no energy spectrum exists. We use this result to constrain the scrambling of information in interacting many-body systems. For Hamiltonian systems, we show that the fundamental question of the fastest possible scrambling time-without any restrictions on the structure of interactions-maps to a purely mathematical property of the density of states involving the non-negativity of Fourier transforms. We illustrate these bounds in the Sachdev-Ye-Kitaev model, where we show that despite its "maximally chaotic" nature, the sustained scrambling of sufficiently large fermion subsystems via entanglement generation requires an exponentially long time in the subsystem size.

Mean performances, character associations and multi-environmental evaluation of chilli landraces in north western Himalayas.

Even though many varieties have been recommended across agro-climate zones of Himachal Pradesh, yet the information on stability is lacking in this State. Hence, the present investigation was carried out to identify high yielding stable genotypes among various pre-adapted landraces. The material consists of 20 chilli landraces including check i.e. DKC-8. The experiment was laid out in a RCBD. The data were recorded and analyzed to work out mean performances and the inferences were drawn for parameters of variability, correlation coefficients, path coefficients and stability analysis. As per mean performances, CS7 and CS9 were earliest in flowering, CS13 is earliest in days to ripe maturity, CS10 had highest plant height and CS9 had highest average fruit weight and ripe fruit yield plant-1. High PCV and GCV were recorded for ripe fruit yield plant-1. Heritability and genetic advance were recorded maximum for plant height in summer seasons and were recorded maximum for number of ripe fruits plant-1 in winter season. Correlation coefficients showed that number of ripe fruits plant-1 and average ripe fruit weight were positively and significantly correlated with ripe fruit yield plant-1. Path coefficient analysis in summer and winter seasons showed that average ripe fruit weight had the highest positive direct effect on ripe fruit yield plant-1. The pooled data over environments were analyzed to estimate the interaction effects between genotypes × environment. The mean sum of squares due to genotypes, environments and genotypes × environment interaction were significant for all the characteristics. CS1, CS3, CS6, CS10, CS13, CS15 were adapted to all environments, CS7 and CS9 were specifically adapted to favourable environment and CS2 was specifically adapted to unfavorable environment for 50% flowering, landraces CS1, CS2 and CS3were well adapted to all environments for ripe maturity whereas landraces CS6, CS10 and CS19 were well adapted to all environment for number of ripe fruit and ripe fruit yield.

Phage Biocontrol Effectively Reduces Contamination of Wheat with Shiga Toxin-producing Escherichia coli O121 and O26 Without Adverse Effects on Flour Quality.

Contamination of wheat flours with Shiga toxin-producing E. coli (STEC) is a concern for the milling industry. Milling-specific interventions are needed to address this food safety hazard. The objectives for this study were to determine the efficacy of bacteriophage treatment in reducing wheat STEC contamination during tempering, and assess its effects on flour milling and baking quality. Bacteriophage solutions were prepared by mixing sterile water with the bacteriophage treatment at the following levels: 1 × 106 (0.1%), 2.5 × 106 (0.25%), 5 × 106 (0.5%), 1 × 107 (1.0%), and 1 × 108 (10%) PFU/g wheat dosage. Sterile water (0%) was used as the control. Predried wheat grains were inoculated with STEC (O121 and O26) at 5.0 and 6.0 log CFU/g to restore its original moisture content followed by resting for 24 h. Inoculated grains were then tempered (16% moisture, 24 h) using the prepared bacteriophage solutions. Grains were sampled at 0.5, 1, 2, 6, 12, 18, and 24 h during tempering to determine STEC concentration. The effects of the phage solutions on the flour milling and baking quality were also tested. Tempering time, bacteriophage dose, and their interaction had significant effects on phage efficacy (P < 0.05), with better reductions observed at longer tempering times and higher bacteriophage doses. The use of phage solutions reduced (P < 0.05) wheat STEC concentration after tempering, with the 10% treatment (3.2 logs) achieving ahigher reduction than the 1% (2.4 logs) treatment under similar phage preparation. Phage tempering (including at the highest concentration examined, i.e., 10%) produced wheat flours with comparable quality to the control. Phage-treated wheat flour resulted in breads with finer crumb structure, and comparable texture compared to the control. Phage tempering is a viable intervention for wheat milling as it reduced STEC loads of wheat with no detrimental effects to flour milling and baking quality.

Phage biocontrol for reducing bacterial foodborne pathogens in produce and other foods.

Foodborne pathogen contamination causes approximately 47 million cases of foodborne illness in the United States and renders thousands of pounds of food products inedible, aggravating the already dire situation of food loss. Reducing foodborne contamination not only improves overall global public health but also reduces food waste and loss. Phage biocontrol or phage-mediated reduction of bacterial foodborne pathogens in various foods has been gaining interest recently as an effective and environmentally friendly food-safety approach. Consequently, several commercial phage-based food-safety products have been developed and are increasingly implemented by the food industry in the United States. This review focuses on the use of phage biocontrol in mitigating bacterial pathogen contamination in various food products with a special emphasis on applications to fresh produce.

Resistomes and microbiome of meat trimmings and colon content from culled cows raised in conventional and organic production systems.

BACKGROUND: The potential to distribute bacteria resistant to antimicrobial drugs in the meat supply is a public health concern. Market cows make up a fifth of the U.S. beef produced but little is known about the entire population of bacteria (the microbiome) and entirety of all resistance genes (the resistome) that are found in this population. The objective of this study was to characterize and compare the resistomes and microbiome of beef, dairy, and organic dairy market cows at slaughter. METHODS: Fifty-four (N = 54) composite samples of both colon content and meat trimmings rinsate samples were collected over six visits to two harvest facilities from cows raised in three different production systems: conventional beef, conventional dairy, and organic dairy (n = 3 samples per visit per production system). Metagenomic DNA obtained from samples were analyzed using target-enriched sequencing (resistome) and 16S rRNA gene sequencing (microbiome). RESULTS: All colon content samples had at least one identifiable antimicrobial resistance gene (ARG), while 21 of the 54 meat trimmings samples harbored at least one identifiable ARGs. Tetracycline ARGs were the most abundant class in both colon content and carcass meat trimmings. The resistome found on carcass meat trimmings was not significantly different by production system (P = 0.84, R2 = 0.00) or harvest facility (P = 0.10, R2 = 0.09). However, the resistome of colon content differed (P = 0.01; R2 = 0.05) among production systems, but not among the harvest facilities (P = 0.41; R2 = 0.00). Amplicon sequencing revealed differences (P < 0.05) in microbial populations in both meat trimmings and colon content between harvest facilities but not production systems (P > 0.05). CONCLUSIONS: These data provide a baseline characterization of an important segment of the beef industry and highlight the effect that the production system where cattle are raised and the harvest facilities where an animal is processed can impact associated microbiome and resistomes.

Phage Biocontrol Applications in Food Production and Processing.

Bacteriophages, or phages, are one of the most, if not the most, ubiquitous organisms on Earth. Interest in various practical applications of bacteriophages has been gaining momentum recently, with perhaps the most attention (and most regulatory approvals) focused on their use to improve food safety. This approach, termed 'phage biocontrol' or 'bacteriophage biocontrol', includes both pre- and post-harvest application of phages as well as decontamination of the food contact surfaces in food processing facilities. This review focuses on post-harvest applications of phage biocontrol, currently the most commonly used type of phage mediation. We also briefly describe various commercially available phage preparations and discuss the challenges still facing this novel yet promising approach.

Antimicrobial Resistance in U.S. Retail Ground Beef with and without Label Claims Regarding Antibiotic Use.

ABSTRACT: Antibiotics used during food animal production account for approximately 77% of U.S. antimicrobial consumption by mass. Ground beef products labeled as raised without antibiotics (RWA) are perceived to harbor lower levels of antimicrobial-resistant bacteria than conventional (CONV) products with no label claims regarding antimicrobial use. Retail ground beef samples were obtained from six U.S. cities. Samples with an RWA or U.S. Department of Agriculture Organic claim (n = 299) were assigned to the RWA production system. Samples lacking these claims (n = 300) were assigned to the CONV production system. Each sample was cultured for the detection of five antimicrobial-resistant bacteria. Genomic DNA was isolated from each sample, and a quantitative PCR assay was used to determine the abundance of 10 antimicrobial resistance (AMR) genes. Prevalence of tetracycline-resistant Escherichia coli (CONV, 46.3%; RWA, 34.4%; P < 0.01) and erythromycin-resistant Enterococcus (CONV, 48.0%; RWA, 37.5%; P = 0.01) was higher in CONV ground beef. Salmonella was detected in 1.2% of samples. The AMR gene blaCTX-M (CONV, 4.1 log-normalized abundance; RWA, 3.8 log-normalized abundance; P < 0.01) was more abundant in CONV ground beef. The AMR genes mecA (CONV, 4.4 log-normalized abundance; RWA, 4.9 log-normalized abundance; P = 0.05), tet(A) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), tet(B) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), and tet(M) (CONV, 5.4 log-normalized abundance; RWA, 5.8 log-normalized abundance; P < 0.01) were more abundant in RWA ground beef. Although these results suggest that antimicrobial use during U.S. cattle production does not increase human exposure to antimicrobial-resistant bacteria via ground beef, quantitative microbiological risk assessments are required for authoritative determination of the human health impacts of the use of antimicrobial agents during beef production.

Antimicrobial Resistance at Two U.S. Cull Cow Processing Establishments.

ABSTRACT: Culled beef cows (cows that have reached the end of their productive life span in cow-calf operations) and culled dairy cows represent approximately 18% of the cattle harvested in the United States annually, but data on antimicrobial resistance (AMR) in these cull cattle are extremely limited. To address this data gap, colon contents were obtained from 180 culled conventional beef cows, 179 culled conventional dairy cows, and 176 culled organic dairy cows (produced without using antimicrobials). Sponge samples were also collected from 181 conventional beef, 173 conventional dairy, and 180 organic dairy cow carcasses. These samples were obtained on 6 days (3 days each at two beef harvest and processing establishments). At one establishment, 30 samples of beef manufacturing trimmings from conventional cows and 30 trim samples from organic dairy cows were acquired. All 1,129 samples were cultured for Escherichia coli, tetracycline-resistant (TETr) E. coli, third-generation cephalosporin-resistant (3GCr) E. coli, Salmonella, and 3GCrSalmonella. Metagenomic DNA was isolated from 535 colon content samples, and quantitative PCR assays were performed to assess the abundances of the following 10 antimicrobial resistance genes: aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). For colon contents, only TETrE. coli (P < 0.01), 3GCrE. coli (P < 0.01), and erm(B) (P = 0.03) levels were higher in conventional than in organic cows. Sampling day also significantly affected (P < 0.01) these levels. Production system did not affect the levels of any measured AMR on carcasses or trim. The human health impact of the few significant AMR differences could not be determined due to the lack of standards for normal, background, safe, or basal values. Study results provide key heretofore unavailable data that may inform quantitative microbial risk assessments to address these gaps.

Phage Biocontrol Improves Food Safety by Significantly Reducing the Level and Prevalence of Escherichia coli O157:H7 in Various Foods.

ABSTRACT: Management of Shiga toxin-producing Escherichia coli (STEC), including E. coli O157:H7, in food products is a major challenge for the food industry. Several interventions, such as irradiation, chemical disinfection, and pasteurization, have had variable success controlling STEC contamination. However, these interventions also indiscriminately kill beneficial bacteria in foods, may impact organoleptic properties of foods, and are not always environmentally friendly. Biocontrol using bacteriophage-based products to reduce or eliminate specific foodborne pathogens in food products has been gaining attention due to the specificity, safety, and environmentally friendly properties of lytic bacteriophages. We developed EcoShield PX, a cocktail of lytic bacteriophages, that specifically targets STEC. This study was conducted to examine the efficacy of this bacteriophage cocktail for reducing the levels of E. coli O157:H7 in eight food products: beef chuck roast, ground beef, chicken breast, cooked chicken, salmon, cheese, cantaloupe, and romaine lettuce. The food products were challenged with E. coli O157:H7 at ca. 3.0 log CFU/g and treated with the bacteriophage preparation at ca. 1 × 106, 5 × 106, or 1 × 107 PFU/g. Application of 5 × 106 and 1 × 107 PFU/g resulted in significant reductions (P < 0.05) in E. coli O157:H7 levels of up to 97% in all foods. When bacteriophages (ca. 1 × 106 PFU/g) were used to treat lower levels of E. coli O157:H7 (ca. 1 to 10 CFU/10 g) on beef chuck roast samples, mimicking the levels of STEC found under real-life conditions in food processing plants, the prevalence of STEC in the samples was significantly reduced (P < 0.05) by ≥80%. Our results suggest that this STEC-targeting bacteriophage preparation can result in significant reduction of both the levels and prevalence of STEC in various foods and, therefore, may help improve the safety and reduce the risk of recalls of foods at high risk for STEC contamination.

In-Feed Tylosin Phosphate Administration to Feedlot Cattle Minimally Affects Antimicrobial Resistance.

ABSTRACT: The macrolide class antimicrobial tylosin (trade name Tylan) is approved by the U.S. Food and Drug Administration for continuous inclusion in feed for liver abscess prevention. To address concerns that this antimicrobial application may threaten human health, a population of feedlot steers was split into a control treatment (n = 42) and a tylosin treatment (n = 42). Feed rations were identical except for the inclusion of tylosin at 60 to 90 mg per head per day. Fecal swab (n = 335), pen surface material (n = 256), feed (n = 56), and water trough (n = 32) samples were obtained over four sample occasions: November (1 day before the start of tylosin inclusion in feed), January (80 days of tylosin in feed), April (167 days), and June (253 days). These samples were cultured for Escherichia coli, tetracycline-resistant E. coli, third-generation cephalosporin-resistant E. coli, Enterococcus, tetracycline-resistant Enterococcus, and erythromycin-resistant Enterococcus. Metagenomic DNA was isolated from each June fecal swab and pen surface material sample. Metagenomic DNA samples were pooled by pen for 14 fecal and 14 pen surface material samples. Quantitative PCR was employed to assess the abundances of the following 10 antimicrobial resistance genes: aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). Nasal swab samples (n = 335) were obtained from each steer during each sample period and cultured for the presence of Staphylococcus aureus and methicillin-resistant S. aureus. Of these measurements, only January and June mean fecal swab erythromycin-resistant Enterococcus colony counts for tylosin-treated cattle were significantly higher (P ≤ 0.05) than the range of mean values for control treatments. These results suggest that in-feed tylosin through the end of finishing has a narrow and minimal antimicrobial resistance impact.

Many-Body Level Statistics of Single-Particle Quantum Chaos.

We consider a noninteracting many-fermion system populating levels of a unitary random matrix ensemble (equivalent to the q=2 complex Sachdev-Ye-Kitaev model)-a generic model of single-particle quantum chaos. We study the corresponding many-particle level statistics by calculating the spectral form factor analytically using algebraic methods of random matrix theory, and match it with an exact numerical simulation. Despite the integrability of the theory, the many-body spectral rigidity is found to have a surprisingly rich landscape. In particular, we find a residual repulsion of distant many-body levels stemming from single-particle chaos, together with islands of level attraction. These results are encoded in an exponential ramp in the spectral form factor, which we show to be a universal feature of nonergodic many-fermion systems embedded in a chaotic medium.

Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato.

Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries. Despite having considerably high productivity, continuous supply as per the market demand is hard to achieve, mostly because of periodic losses occurring due to biotic as well as abiotic stresses. Although tomato is a temperate crop, it is grown in almost all the climatic zones because of widespread demand, which makes it challenge to adapt in diverse conditions. Development of tomato cultivars with enhanced abiotic stress tolerance is one of the most sustainable approaches for its successful production. In this regard, efforts are being made to understand the stress tolerance mechanism, gene discovery, and interaction of genetic and environmental factors. Several omics approaches, tools, and resources have already been developed for tomato growing. Modern sequencing technologies have greatly accelerated genomics and transcriptomics studies in tomato. These advancements facilitate Quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). However, limited efforts have been made in other omics branches like proteomics, metabolomics, and ionomics. Extensive cataloging of omics resources made here has highlighted the need for integration of omics approaches for efficient utilization of resources and a better understanding of the molecular mechanism. The information provided here will be helpful to understand the plant responses and the genetic regulatory networks involved in abiotic stress tolerance and efficient utilization of omics resources for tomato crop improvement.

Food Service Pork Chops from Three U.S. Regions Harbor Similar Levels of Antimicrobial Resistance Regardless of Antibiotic Use Claims.

Pork products from animals "raised without antibiotics" (RWA) are assumed to harbor lower levels of antimicrobial resistance (AMR) than conventional (CONV) pork products with no claims regarding use of antimicrobial agents during production. A total of 372 pork chop samples from CONV (n = 190) and RWA (n = 182) production systems were collected over 13 months from three food service suppliers. The following bacteria were cultured: Escherichia coli, tetracycline-resistant (TETr) E. coli, third-generation cephalosporin-resistant (3GCr) E. coli, Salmonella enterica, TETr Salmonella, 3GCr Salmonella, nalidixic acid-resistant Salmonella, Enterococcus spp., TETr Enterococcus, erythromycin-resistant Enterococcus, Staphylococcus aureus, and methicillin-resistant S. aureus. Production system did not significantly impact the detection of cultured bacteria (P > 0.05). Metagenomic DNA was isolated from each sample, and equal amounts of metagenomic DNA were pooled by supplier, month, and production system for 75 pooled samples (38 CONV, 37 RWA). Quantitative PCR was used to assess the abundances of the following 10 AMR genes: aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). For all 10 AMR genes, abundances did not differ significantly (P > 0.05) between production systems. These results suggest that use of antimicrobial agents during swine production minimally impacts the AMR of bacteria in pork chops.

Upregulation of peroxide scavenging enzymes and multidrug efflux proteins highlight an active sodium hypochlorite response in Pseudomonas fluorescens biofilms.

The oxidative biocide sodium hypochlorite is among the most commonly used antimicrobial agents in the control of surface-attached microbial communities (biofilms). Clarifying the genetic response of microorganisms in biofilms to hypochlorite may contribute to improved biofilm control strategies. Here, RNA-seq was used to investigate the differential gene expression response of industrially relevant Pseudomonas fluorescens biofilms to sub-lethal concentrations of sodium hypochlorite. Pseudomonas biofilms responded to hypochlorite exposure with increased transcription of genes encoding peroxide scavenging enzymes (e.g., alkyl hydroperoxide reductase (Ahp) and hydroperoxide resistance protein (Ohr)), oxidative stress repair enzymes (e.g., the periplasmic sulfoxide reductase YedYZ complex), and multidrug efflux (e.g., MexEF pumps). In addition, genes involved in amino acid synthesis and energy metabolism were down-regulated following hypochlorite exposure. This work improves the current understanding of genetic response mechanisms to biocides and contributes to the optimization of biocides and application strategies.

Similar Levels of Antimicrobial Resistance in U.S. Food Service Ground Beef Products with and without a "Raised without Antibiotics" Claim.

U.S. ground beef with "raised without antibiotics" (RWA) label claims are perceived as harboring fewer bacteria with antimicrobial resistance (AMR) than are found in conventional (CONV) ground beef with no such label claim. A total of 370 ground beef samples from CONV ( n = 191) and RWA ( n = 179) production systems were collected over 13 months from three food service suppliers. The following bacteria were cultured: Escherichia coli, tetracycline-resistant (TETr) E. coli, third-generation cephalosporin-resistant (3GCr) E. coli, Salmonella enterica, TETr S. enterica, 3GCr S. enterica, nalidixic acid-resistant S. enterica, Enterococcus spp., erythromycin-resistant Enterococcus spp., TETr Enterococcus spp., Staphylococcus aureus, and methicillin-resistant S. aureus. TETr E. coli was more frequently detected in CONV ground beef (CONV, 54.2%; RWA, 35.2%; P < 0.01), but supplier ( P < 0.01) and production system × suppler interaction ( P < 0.01) effects were also significant. Metagenomic DNA was isolated from each sample, and equal amounts of metagenomic DNA were pooled by supplier, month, and production system for 75 pooled samples (38 CONV, 37 RWA). The abundance of aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M) genes was assessed by quantitative PCR. The tet(A) (2.9-log2-fold change, P = 0.04) and tet(B) (5.6-log2-fold change) ( P = 0.03) genes were significantly more abundant in RWA ground beef. Phylogenetic analyses revealed that ground beef microbiomes differed more by supplier than by production system. These results were consistent with prior research suggesting antimicrobial use in U.S. beef cattle has minimal impact on the AMR of bacteria found in these products. These results should spur a reevaluation of assumptions regarding the impact of antimicrobial use during U.S. beef production on the AMR of bacteria in ground beef.

Effects of In-Feed Chlortetracycline Prophylaxis in Beef Cattle on Antimicrobial Resistance Genes.

Approximately 20% of U.S. beef cattle receive prophylactic in-feed administration of chlortetracycline (CTC) to reduce bovine respiratory disease (BRD) incidence during the transition into feedlots. To determine the impact of prophylaxis on selected antimicrobial resistance genes (ARGs), 300 beef cattle were placed into 10 pens (30 head/pen). Five "CTC group" pens received in-feed CTC (10 mg/lb of body weight/d) from the fifth to ninth day after feedlot arrival, whereas the five "Control group" pens received no CTC. Fecal swabs and pen surface materials were collected for metagenomic DNA isolation on five sample occasions: arrival at the feedlot, 5 d posttreatment (dpt), and 27, 75, and 117 dpt. For each sample occasion, fecal samples and pen surface material samples were pooled by pen. Quantitative polymerase chain reaction was used to determine the abundances of 10 ARGs. Due to low detection percentages (%D) and quantification percentages (%Q), the abundances of five ARGs were not analyzed: aac(6')-Ie-aph(2'') (%D = 43%, %Q = 4%), blaCMY-2 (%D = 41%, %Q = 0%), blaCTX-M (%D = 0%, %Q = 0%), blaKPC-2 (%D = 21%, %Q = 16%), and mecA (%D = 4%, %Q = 0%). The %D and %Q for the ARGs aadA1, erm(B), tet(A), tet(B), and tet(M) were ≥98% and ≥90%, respectively. The abundances of aadA1, erm(B), tet(A), tet(B), and tet(M) resistance genes did not differ (p > 0.05) between the CTC and control groups at any sampling time for feces or pen surface material. Although only 10 ARGs were examined in this study, the results suggest that a single 5-d in-feed CTC prophylaxis of beef cattle to prevent BRD has a negligible impact on the abundances of ARGs.

Microbial communities in Bakken region produced water.

The Bakken Shale has become one of the United States' most important oil and gas producing regions. This study examined the microbiology and geochemical characteristics of Bakken region produced water from 17 well sites sampled from the three-phase separator and produced water holding tank over a 6-month time frame. Produced water samples had high total dissolved solids (220 000-350 000 mg/L) and low dissolved organic carbon concentrations (41-132 mg/L). Microbial abundances varied between 101 and 104 16S rRNA gene copies/mL, approximately four orders of magnitude below those observed for produced waters from other hydraulic fracturing regions. The most abundant bacterial orders found in produced water samples were Bacillales, Halanaerobiales and Pseudomonadales, consistent with observations from other unconventional resource plays. Our observations suggest temporal community structuring, as produced waters sampled early in our sampling period were dominated by Halanaerobiales, and produced waters sampled at the remaining winter sampling time points were characterized by high relative abundances of Bacillales and Pseudomonadales. Data from this study extends the current available knowledge of the microbiology and chemistry associated with produced water from the Bakken region and provides insights into microbial community dynamics in hypersaline subsurface fluids.

Functional blaKPC-2 Sequences Are Present in U.S. Beef Cattle Feces Regardless of Antibiotic Use.

Carbapenems are classified as critically important antibiotics since they are employed when resistant Gram-negative bacterial infections fail to respond to other antibiotic therapies. Carbapenem-resistant bacteria (CRB) were traditionally understood to be rare in the U.S. food-producing animals. Recently, using quantitative polymerase chain reaction (qPCR), our group detected blaKPC-2 in all 72 metagenomic DNA (mgDNA) samples prepared from the feces of 36 lots of beef cattle "raised without antibiotics" (RWA) and 36 lots raised "conventionally" (CONV). Since a small internal fragment of the blaKPC-2 gene was targeted by the qPCR detection method, we sought to determine if functional blaKPC-2-like sequences are present in beef cattle feces. Full-length blaKPC-2 sequences were amplified from 18 mgDNA samples (9 CONV and 9 RWA), cloned into pCR4Blunt-TOPO vectors, and transformed into Escherichia coli TOP10 cells. All 14 of the samples with blaKPC-2 cloned in the same orientation as the Plac promoter had carbapenemase activity and imipenem minimum inhibitory concentrations ≥32 µg/mL. We conclude that the blaKPC-2 genes detected in our previous study were functional, which indicates that CRB were present in those fecal samples. Identification of functional Klebsiella pneumoniae carbapenemases in fecal samples from both CONV and RWA cattle strongly suggests that CRB are more common in U.S. beef cattle feces than previously believed. Critically, more research using similar qPCR methods to determine the levels of carbapenem-resistant genes in human feces, feces from other food animal species, wildlife, companion animals, and the environment are required to accurately assess public health implications.

Impact of "Raised without Antibiotics" Beef Cattle Production Practices on Occurrences of Antimicrobial Resistance.

The specific antimicrobial resistance (AMR) decreases that can be expected from reducing antimicrobial (AM) use in U.S. beef production have not been defined. To address this data gap, feces were recovered from 36 lots of "raised without antibiotics" (RWA) and 36 lots of "conventional" (CONV) beef cattle. Samples (n = 719) were collected during harvest and distributed over a year. AMR was assessed by (i) the culture of six AM-resistant bacteria (ARB), (ii) quantitative PCR (qPCR) for 10 AMR genes (ARGs), (iii) a qPCR array of 84 ARGs, and (iv) metagenomic sequencing. Generally, AMR levels were similar, but some were higher in CONV beef cattle. The prevalence of third-generation cephalosporin-resistant (3GCr) Escherichia coli was marginally different between production systems (CONV, 47.5%; RWA, 34.8%; P = 0.04), but the seasonal effect (summer, 92.8%; winter, 48.3%; P < 0.01) was greater. Erythromycin-resistant (ERYr) Enterococcus sp. concentrations significantly differed between production systems (CONV, 1.91 log10 CFU/g; RWA, 0.73 log10 CFU/g; P < 0.01). Levels of aadA1, ant(6)-I, bla ACI, erm(A), erm(B), erm(C), erm(F), erm(Q), tet(A), tet(B), tet(M), and tet(X) ARGs were higher (P < 0.05) in the CONV system. Aggregate abundances of all 43 ARGs detected by metagenomic sequencing and the aggregate abundances of ARGs in the aminoglycoside, ß-lactam, macrolide-lincosamide-streptogramin B (MLS), and tetracycline AM classes did not differ (log2 fold change < 1.0) between CONV and RWA systems. These results suggest that further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.IMPORTANCE The majority of antimicrobial (AM) use in the United States is for food-animal production, leading to concerns that typical AM use patterns during "conventional" (CONV) beef cattle production in the United States contribute broadly to antimicrobial resistance (AMR) occurrence. In the present study, levels of AMR were generally similar between CONV and "raised without antibiotics" (RWA) cattle. Only a limited number of modest AMR increases was observed in CONV cattle, primarily involving macrolide-lincosamide-streptogramin B (MLS) and tetracycline resistance. Macrolides (tylosin) and tetracyclines (chlortetracycline) are administered in-feed for relatively long durations to reduce liver abscesses. To ensure judicious AM use, the animal health, economic, and AMR impacts of shorter duration in-feed administration of these AMs should be examined. However, given the modest AMR reductions observed, further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure.

Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.