CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure

The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system CRISPR-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its anti-plasmid efficacy in an agricultural niche - manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach.

Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum β-Lactamase in Escherichia coli from Different Animal Sources

Antimicrobial resistance associated with the spread of plasmid-encoded extended-spectrum β-lactamase (ESBL) genes conferring resistance to third generation cephalosporins is increasing worldwide. However, data on the population of ESBL producing E. coli in different animal sources and their antimicrobial characteristics are limited. The purpose of this study was to investigate potential reservoirs of ESBL-encoded genes in E. coli isolated from swine, beef, dairy, and poultry collected from different regions of the United States using whole-genome sequencing (WGS). Three hundred isolates were typed into different phylogroups, characterized by BOX AIR-1 PCR and tested for resistance to antimicrobials. Of the 300 isolates, 59.7% were resistant to sulfisoxazole, 49.3% to tetracycline, 32.3% to cephalothin, 22.3% to ampicillin, 20% to streptomycin, 16% to ticarcillin; resistance to the remaining 12 antimicrobials was less than 10%. Phylogroups A and B1 were most prevalent with A (n = 92, 30%) and B1 (87 = 29%). A total of nine E. coli isolates were confirmed as ESBL producers by double-disk synergy testing and multidrug resistant (MDR) to at least three antimicrobial drug classes. Using WGS, significantly higher numbers of ESBL-E. coli were detected in swine and dairy manure than from any other animal sources, suggesting that these may be the primary animal sources for ESBL producing E. coli. These isolates carry plasmids, such as IncFIA(B), IncFII, IncX1, IncX4, IncQ1, CollRNAI, Col440I, and acquired ARGs aph(6)-Id, aph(3″)-Ib, aadA5, aph(3')-Ia, bla_CTX-M-15, bla_TEM-1B, mphA, ermB, catA1, sul1, sul2, tetB, dfrA17. One of the E. coli isolates from swine with ST 410 was resistant to nine antibiotics and carried more than 28 virulence factors, and this ST has been shown to belong to an international high-risk clone. Our data suggests that ESBL producing E. coli are widely distributed in different animal sources, but swine and dairy cattle may be their main reservoir.

Corn stalk residue may add antibiotic-resistant bacteria to manure composting piles

Manure is commonly used as a fertilizer or soil conditioner; however, land application of untreated manure may introduce pathogens and antibiotic-resistant bacteria (ARB) into the soil, with harmful implications for public health. Composting is a manure management practice wherein a carbon-rich bulking agent, such as corn (Zea mays L.) stalk residue, is added to manure to achieve desirable carbon/nitrogen ratios to facilitate microbial activities and generate enough heat to inactivate pathogens, including antibiotic-resistant pathogens. However, when comparing compost piles and stockpiles for ARB reduction, we noticed that bulking agents added ARB to composting piles and compromised the performance of composting in reducing ARB. We hypothesized that ARB could be prevalent in corn stalk residues, a commonly used bulking agent for composting. To test this hypothesis, corn stalk residue samples throughout Nebraska were surveyed for the presence of ARB. Of the samples tested, 54% were positive for antibiotic-resistant Escherichia coli or enterococci using direct plating or after enrichment. Although not statistically significant, there was a trend wherein the use of pesticides tended to result in a greater prevalence of some ARB. Results from this study suggest that bulking agents can be a source of ARB in manure composting piles and highlight the importance of screening bulking agents for effective ARB reduction in livestock manure during composting.

Recovery of T-cell function in healthy dogs following cessation of oral cyclosporine administration

Cyclosporine is a potent immunosuppressive agent used to treat immune‐mediated disorders in dogs. Secondary infections sometimes necessitate withdrawal of cyclosporine, but it is not known how long it takes for the immune system to recover after cessation of cyclosporine. Our goal was to utilize a validated RT‐qPCR assay in dogs to assess recovery time of the T‐cell cytokines IL‐2 and IFN‐γ after discontinuation of cyclosporine. Six healthy dogs were given oral cyclosporine (10 mg/kg every 12 hr) for 1 week, with samples collected for measurement of cytokine gene expression prior to treatment, and on the last day of therapy. Cyclosporine was then discontinued, and samples were collected daily for an additional 7 days. Results revealed that there was a significant difference in cytokine expression when comparing pre‐treatment and immediate post‐treatment values, corresponding to marked suppression of T‐cell function. There was no significant difference between pre‐treatment values for either cytokine when compared with any day during the recovery period. Cytokine expression, evaluated as a percentage of pre‐treatment baseline samples, demonstrated progressing return of T‐cell function after drug cessation, with full recovery seen in all dogs by Day 4 of the recovery period.

Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

In agricultural systems, interactions between plants and microorganisms are important to maintaining production and profitability. In this study, bacterial communities in floodwaters of rice fields were monitored during the vegetative and reproductive stages of rice plant development using 16S amplicon sequencing. The study was conducted in the south of Brazil, during the crop years 2011/12 and 2012/13. Comparative analyses showed strong differences between the communities of floodwaters associated with the two developmental stages. During the vegetative stage, 1551 operational taxonomic units (OTUs) were detected, while less than half that number (603) were identified in the reproductive stage. The higher bacterial richness observed in floodwater collected during the vegetative stage may have been favored by the higher concentration of nutrients, such as potassium, due to rhizodeposition and fertilizer application. Eighteen bacterial phyla were identified in both samples. Both communities were dominated by Gammaproteobacteria. In the vegetative stage, Alphaproteobacteria and Betaproteobacteria were more abundant and, in contrast, Bacilli and Clostridia were the more dominant classes in the reproductive stage. The major bacterial taxa identified have been previously identified as important colonizers of rice fields. The richness and composition of bacterial communities over cultivation time may contribute to the sustainability of the crop.

Environmental Parameters Associated With Stable Fly (Diptera: Muscidae) Development at Hay Feeding Sites

Substrates composed of hay residues, dung, and urine accumulate around winter hay feeding sites in cattle pastures, providing developmental habitats for stable flies. The objective of this study was to relate physiochemical and microbial properties of these substrates to the presence or absence of stable fly larvae. Properties included pH, temperature, moisture, ammonium concentration, electrical conductivity, and numbers of coliform, fecal coliform, Escherichia coli, and Enterococcus bacteria. Each physiochemical sample was classified as a function of belonging to one of the three 2-m concentric zones radiating from the feeder as well as presence or absence of larvae. In total, 538 samples were collected from 13 sites during 2005-2011. Stable fly larvae were most likely to be found in moist, slightly alkaline substrates with high levels of ammonium and low temperature. The probability of larvae being present in a sample was the highest when the moisture content was 347% relative to dry weight and the average pH was 8.4. Larvae were recovered within all zones, with a nonsignificant, but slightly higher, percentage of samples containing larvae taken 2-4 m from the center. All methods used to enumerate bacteria, except total coliform, indicated decreasing concentrations in hay bale residue throughout the summer. In addition to the environmental parameters, cumulative degree day 10°C had a significant effect on the probability of observing stable fly larvae in a sample, indicating that unidentified seasonal effects also influenced immature stable fly populations.

Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets

Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package - Megraft - that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.

A Large Outbreak of Brainerd Diarrhea Associated with a Restaurant in the Red River Valley, Texas

BACKGROUND

In June 1996, an outbreak of chronic diarrhea was reported to the Texas Department of Health (Austin).

METHODS

We initiated active case finding, performed 2 case-control studies, and conducted an extensive laboratory and environmental investigation.

RESULTS

We identified 114 persons with diarrhea that lasted > or = 4 weeks. Symptoms among 102 patients who were studied included urgency (87%), fatigue (86%), fecal incontinence (74%), and weight loss (73%); the median maximum 24-h stool frequency was 15 stools. Diarrhea persisted for > 6 months in 87% and for > 1 year in 70% of patients who were observed. Fifty-one (89%) of 57 ill persons had eaten at a particular restaurant within 4 weeks before onset, compared with 8 (14%) of 59 matched control subjects (matched odds ratio [OR], undefined; 95% confidence interval [CI], 11.2-infinity). At the restaurant, patients were more likely than their unaffected dining companions to have drunk tap water (OR, 2.8; 95% CI, 1.0-9.9) and to have eaten several specific food items, and they were less likely to have drunk iced tea made from boiled water and store-bought ice (OR, 0.3; 95% CI, 0.05-1.0). A multivariable model that included consumption of tap water and salad bar tomatoes best fit the data. The restaurant had multiple sanitary and plumbing deficiencies. Extensive laboratory and environmental testing for bacterial, parasitic, mycotic, and viral agents did not identify an etiologic agent.

CONCLUSIONS

The clinical, laboratory, and epidemiologic findings are consistent with those of previous outbreaks of Brainerd diarrhea. To our knowledge, this is the largest reported outbreak of Brainerd diarrhea associated with a restaurant.

Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing

OBJECTIVE

To determine whether a selected set of 20 single nucleotide polymorphism (SNP) markers derived from beef cattle populations can be used to verify sample tracking in a commercial slaughter facility that processes primarily market (ie, culled) dairy cows.

DESIGN

Prospective, blinded validation study.

ANIMALS

165 cows and 3 bulls from 18 states (82% Holstein, 8% other dairy breeds, and 10% beef breeds).

PROCEDURE

Blood was collected by venipuncture from randomly chosen animals just prior to slaughter. The purported corresponding liver samples were collected during beef processing, and genotype profiles were obtained for each sample.

RESULTS

On the basis of SNP allele frequencies in these cattle, the mean probability that 2 randomly selected individuals would possess identical genotypes at all 20 loci was 4.3 x 10(-8). Thus, the chance of a coincidental genotype match between 2 animals was 1 in 23 million. Genotype profiles confirmed appropriate matching for 152 of the 168 (90.5%) purported blood-liver sample pairs and revealed mismatching for 16 (9.5%) pairs. For the 16 mismatched sample pairs, 33% to 76% of the 20 SNP genotypes did not match (mean, 52%). Discordance that could be attributed to genotyping error was estimated to be < 1% on the basis of results for split samples.

CONCLUSIONS AND CLINICAL RELEVANCE

Results suggest that this selected set of 20 bovine SNP markers is sufficiently informative to verify accuracy of sample tracking in slaughter plants that process beef or dairy cattle. These or similar SNP markers may facilitate high-throughput, DNA-based, traceback programs designed to detect drug residues in tissues, control of animal diseases, and enhance food safety.