Fonds de Recherche du Québec – Nature et Technologies

A simple solvent-free mechanochemical procedure enables rapid and high-yielding oxidative halogenation of model organometallic Re(I) compounds with excellent and tunable stereoselectivity, demonstrating how mechanochemistry can advance and simplify fundamental organometallic transformations.

Antimicrobial resistance (AMR) is an important burden for public health and veterinary medicine. For Québec (Canada) dairy farms, the prevalence of AMR is mostly described using passive surveillance, which may be misleading. In addition, the presence of extended spectrum β-lactamase (ESBL)/AmpC producing Escherichia coli is unknown. This observational cross-sectional study used random dairy farms ( n = 101) to investigate AMR and extended spectrum β-lactamase (ESBL)/AmpC producing Escherichia coli . Twenty antimicrobials were tested on E. coli isolates ( n = 593) recovered from fecal samples ( n = 599) from calves, cows, and the manure pit. Isolates were mostly susceptible (3% AMR or less) to the highest priority critically important antimicrobials in humans. The highest levels of AMR were to tetracycline (26%), sulfisozaxole (23%) and streptomycin (19%). The resistance genes responsible for these resistances were, respectively : tet (A) , tet (B), sul 1 , sul 2 , sul 3 , aph( 3” )-Ib (str A ), aph( 6 )-Id (str B ), aad A1 , aad A2, and aad A5. ESBL analysis revealed two predominant phenotypes: AmpC (51%) and ESBL (46%) where bla CMY−2 and bla CTX−M ( bla CTX−M−1 , bla CTX−M−15 , and bla CTX−M−55) were the genes responsible for these phenotypes, respectively. During this study, 85% of farms had at least one ESBL/AmpC producing E. coli . Isolates from calves were more frequently resistant than those from cows or manure pits. Although prevalence of AMR was low for critically important antimicrobials, there was a high prevalence of ESBL/AmpC-producing E. coli on Quebec dairy farms, particularly in calves. Those data will help determine a baseline for AMR to evaluate impact of initiatives aimed at reducing AMR.

Abstract In 2021, a catalog of 536 fast radio bursts (FRBs) detected with the Canadian Hydrogen Intensity Mapping Experiment (CHIME) radio telescope was released by the CHIME/FRB Collaboration. This large collection of bursts, observed with a single instrument and uniform selection effects, has advanced our understanding of the FRB population. Here we update the results for 140 of these FRBs for which channelized raw voltage (“baseband”) data are available. With the voltages measured by the telescope’s antennas, it is possible to maximize the telescope sensitivity in any direction within the primary beam, an operation called “beamforming.” This allows us to increase the signal-to-noise ratios of the bursts and to localize them to subarcminute precision. The improved localizations are also used to correct the beam response of the instrument and to measure fluxes and fluences with an ∼10% uncertainty. Additionally, the time resolution is increased by 3 orders of magnitude relative to that in the first CHIME/FRB catalog, and, applying coherent dedispersion, burst morphologies can be studied in detail. Polarization information is also available for the full sample of 140 FRBs, providing an unprecedented data set to study the polarization properties of the population. We release the baseband data beamformed to the most probable position of each FRB. These data are analyzed in detail in a series of accompanying papers.

Quantification of antimicrobial usage (AMU) is crucial to measure the effect of intervention programs, to determine associations between usage and resistance, to compare populations, and for benchmarking purposes. The primary objective of the study was to describe quantitatively the AMU on Quebec dairy farms over 1 yr: (1) the total AMU, (2) the AMU per administration route (intramammary, injectable, oral, intrauterine), and (3) the AMU per antimicrobial class and according to the categorizations of Health Canada and the World Health Organization. The secondary objective was to assess the effect of several characteristics (herd size, level of milk production, and incidence rate of common infectious diseases) on AMU rate. The AMU data were obtained for 101 dairy farms randomly selected in 3 important Quebec dairy regions by collecting and recording all empty drug packaging and invoices for medicated feed (spring 2017 to spring 2018). The AMU rate was reported in number of Canadian defined course doses for cattle per 100 cow-years. The average herd size was 67 cows per farm, and 2/101 farms were certified organic. Overall, an estimated mean of 537 Canadian defined course doses for cattle/100 cow-years was observed. The intramammary route during lactation was the most frequently observed, followed, in decreasing order of usage, by oral route in the feed, intramammary route at drying-off, and injectable route. Oral (other than in animal feed) and intrauterine formulations were infrequently collected from the garbage cans. The 5 most frequently observed antimicrobial classes were, by decreasing order of usage, ionophores, penicillins, aminocoumarins, aminoglycosides, and polymyxins. Highest priority critically important antimicrobials as defined by the World Health Organization were mainly collected from intramammary formulations during lactation followed by injectable and drying-off intramammary formulations. The herd size was positively associated with the total AMU rate but not with the usage rate of highest priority critically important antimicrobials. Incidence of diseases along with preventive use of antimicrobials (drying-off and medicated feed with antimicrobials) explained 48% of the variance in total AMU rate.

Abstract Carboxylic acids are readily available, structurally diverse and shelf-stable; therefore, converting them to the isoelectronic boronic acids, which play pivotal roles in different settings, would be highly enabling. In contrast to the well-recognised decarboxylative borylation, the chemical space of carboxylic-to-boronic acid transformation via deoxygenation remains underexplored due to the thermodynamic and kinetic inertness of carboxylic C-O bonds. Herein, we report a deoxygenative borylation reaction of free carboxylic acids or their sodium salts to synthesise alkylboronates under metal-free conditions. Promoted by a uniquely Lewis acidic and strongly reducing diboron reagent, bis(catecholato)diboron (B 2 cat 2 ), a library of aromatic carboxylic acids are converted to the benzylboronates. By leveraging the same borylative manifold, a facile triboration process with aliphatic carboxylic acids is also realised, diversifying the pool of available 1,1,2-alkyl(trisboronates) that were otherwise difficult to access. Detailed mechanistic studies reveal a stepwise C-O cleavage profile, which could inspire and encourage future endeavours on more appealing reductive functionalisation of oxygenated feedstocks.

A trimetallic rare-earth cluster-based metal–organic framework is synthesized that emits red, green and blue emission simultaneously.

The emergence of multidrug-resistant bacterial strains worldwide has become a serious problem for public health over recent decades. The increase in antimicrobial resistance has been expanding via plasmids as mobile genetic elements encoding antimicrobial resistance (AMR) genes that are transferred vertically and horizontally. This study focuses on Salmonella enterica, one of the leading foodborne pathogens in industrialized countries. S. enterica is known to carry several plasmids involved not only in virulence but also in AMR. In the current paper, we present an integrated strategy to detect plasmid scaffolds in whole genome sequencing (WGS) assemblies. We developed a two-step procedure to predict plasmids based on i) the presence of essential elements for plasmid replication and mobility, as well as ii) sequence similarity to a reference plasmid. Next, to confirm the accuracy of the prediction in 1750 S. enterica short-read sequencing data, we combined Oxford Nanopore MinION long-read sequencing with Illumina MiSeq short-read sequencing in hybrid assemblies for 84 isolates to evaluate the proportion of plasmid that has been detected. At least one scaffold with an origin of replication (ORI) was predicted in 61.3% of the Salmonella isolates tested. The results indicated that IncFII and IncI1 ORIs were distributed in many S. enterica serotypes and were the most prevalent AMR genes carrier, whereas IncHI2A/IncHI2 and IncA/C2 were more serotype restricted but bore several AMR genes. Comparison between hybrid and short-read assemblies revealed that 81.1% of plasmids were found in the short-read sequencing using our pipeline. Through this process, we established that plasmids are prevalent in S. enterica and we also substantially expand the AMR genes in the resistome of this species.

Low concentrations of cationic silica nanoparticles impact lung surfactant membrane structure while anionic nanoparticles have minimal effect.

Staphylococcus aureus is a major etiological agent of clinical and subclinical bovine mastitis. The versatile and adaptative evolutionary strategies of this bacterium have challenged mastitis control and prevention globally, and the high incidence of S. aureus mastitis increases concerns about antimicrobial resistance (AMR) and zoonosis. This study aims to describe the evolutionary relationship between bovine intramammary infection (IMI)-associated S. aureus and human pathogenic S. aureus and further elucidate the specific genetic composition that leads to the emergence of successful bovine IMI-associated S. aureus lineages. We performed a phylogenomic analysis of 187 S . aureus isolates that originated from either dairy cattle or humans. Our results revealed that bovine IMI-associated S. aureus isolates showed distinct clades compared to human-originated S. aureus isolates. From a pan-genome analysis, 2070 core genes were identified. Host-specific genes and clonal complex (CC)-specific genes were also identified in bovine S. aureus isolates, mostly located in mobile genetic elements (MGEs). Additionally, the genome sequences of three apparent human-adapted isolates (two from CC97 and one from CC8), isolated from bovine mastitis samples, may provide an snapshot of the genomic characteristics in early host spillover events. Virulence and AMR genes were not conserved among bovine IMI-associated S. aureus isolates. Restriction-modification (R-M) genes in bovine IMI-associated S. aureus demonstrated that the Type I R-M system was lineage-specific and Type II R-M system was sequence type (ST)-specific. The distribution of exclusive, virulence, and AMR genes were closely correlated with the presence of R-M systems in S. aureus , suggesting that R-M systems may contribute to shaping clonal diversification by providing a genetic barrier to the horizontal gene transfer (HGT). Our findings indicate that the CC or ST lineage-specific R-M systems may limit genetic exchange between bovine-adapted S. aureus isolates from different lineages.

This article has been retracted. The retraction notice can be found at 10.1099/mgen.0.001343 Escherichia coli is a major causative agent of environmental bovine mastitis and this disease causes significant economic losses for the dairy industry. There is still debate in the literature as to whether mammary pathogenic E. coli (MPEC) is indeed a unique E. coli pathotype, or whether this infection is merely an opportunistic infection caused by any E. coli isolate being displaced from the bovine gastrointestinal tract to the environment and, then, into the udder. In this study, we conducted a thorough genomic analysis of 113 novel MPEC isolates from clinical mastitis cases and 100 bovine commensal E. coli isolates. A phylogenomic analysis indicated that MPEC and commensal E. coli isolates formed clades based on common sequence types and O antigens, but did not cluster based on mammary pathogenicity. A comparative genomic analysis of MPEC and commensal isolates led to the identification of nine genes that were part of either the core or the soft-core MPEC genome, but were not found in any bovine commensal isolates. These apparent MPEC marker genes were genes involved with nutrient intake and metabolism [ adeQ , adenine permease; nifJ , pyruvate-flavodoxin oxidoreductase; and yhjX , putative major facilitator superfamily (MFS)-type transporter], included fitness and virulence factors commonly seen in uropathogenic E. coli ( pqqL , zinc metallopeptidase, and fdeC , intimin-like adhesin, respectively), and putative proteins [ yfiE , uncharacterized helix-turn-helix-type transcriptional activator; ygjI , putative inner membrane transporter; and ygjJ , putative periplasmic protein]. Further characterization of these highly conserved MPEC genes may be critical to understanding the pathobiology of MPEC.

Eu-Tb-UiO-66 acts as a highly sensitive luminescent thermometer near room temperature.

Monitoring antimicrobial usage (AMU) in dairy cattle is becoming common in a growing number of countries, with the ultimate goal to improve practices, reduce the development of antimicrobial resistance, and protect human health. However, antimicrobials delivered as feed additives can be missed by some of the quantification methods usually implemented. Our objective was to compare three methods of quantification of in-feed AMU in Québec dairy herds. We recruited 101 dairy producers for one year in the Québec province. Quantities of antimicrobials were calculated by farm from: (1) feed mills invoices (reference method); (2) veterinary prescriptions; and (3) information collected during an in-person interview of each producer. We standardized AMU rates in kilograms per 100 cow-years and compared the reference method to both alternative methods using concordance correlation coefficients and Bland-Altman plots. Antimicrobial usage was well estimated by veterinary prescriptions (concordance correlation coefficient (CCC) = 0.66) or by the approximation using producer's data (CCC = 0.73) when compared with actual deliveries by feed mills. Users of medically important antimicrobials for human medicine (less than 10% of the farms) were easily identified using veterinary prescriptions. Given that veterinary prescriptions were mostly electronic (90%), this method could be integrated as part of a monitoring system in Québec.

Despite its importance in veterinary medicine, there is little information about antimicrobial resistance (AMR) and its transmission in dairy cattle. The aim of this work is to compare AMR phenotypes and genotypes in resistant Escherichia coli and to determine how the resistance genes spread among the E. coli population on dairy farms in Québec, Canada. From an existing culture collection of E. coli isolated from dairy manure, a convenient selection of the most resistant isolates (a high level of multidrug resistance or resistance to broad-spectrum β-lactams or fluoroquinolones) was analyzed (n = 118). An AMR phenotype profile was obtained for each isolate. Whole genome sequencing was used to determine the presence of resistance genes, point mutations, and mobile genetic elements. In addition, a subset of isolates from 86 farms was taken to investigate the phylogenetic relationship and geographic distribution of the isolates. The average agreement between AMR phenotypes and genotypes was 95%. A third-generation cephalosporin resistance gene (blaCTX-M-15), a resistance gene conferring reduced susceptibility to fluoroquinolones (qnrS1), and an insertion sequence (ISKpn19) were detected in the vicinity of each other on the genome. These genes were harbored in one triplet of clonal isolates from three farms located >100 km apart. Our study reveals the dissemination of resistant E. coli clones between dairy farms. Furthermore, these clones are resistant to broad-spectrum β-lactam and fluoroquinolone antimicrobials.

Metal–organic frameworks (MOFs) are a class of porous materials that are often crystalline with high surface area and structural tunability. In this laboratory experiment designed for inorganic chemistry students at the undergraduate level, students complete a two-step experiment where they will first (i) synthesize two isostructural zirconium-based MOFs, UiO-66 and UiO-67, and then (ii) isolate and characterize the materials using powder X-ray diffraction (PXRD). A simple solvothermal procedure was developed for the synthesis of UiO-66 and UiO-67 using the air/moisture-stable zirconyl chloride octahydrate as a starting reagent. Depending on the equipment available, the MOFs can be further characterized by nitrogen adsorption analysis for surface area determination using Brunauer–Emmett–Teller (BET) theory, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), thermogravimetric analysis (TGA), 1H nuclear magnetic resonance (NMR) spectroscopy, and scanning electron microscopy (SEM). Upon synthesizing the MOFs and collecting the characterization data, students analyze and describe their results by answering a series of questions included in the laboratory manual. This exercise will allow students to develop practical laboratory skills while expanding their knowledge on some fundamental concepts in inorganic chemistry, materials chemistry, MOFs, crystallography, and other characterization techniques as availability allows.

Our first objective was to estimate the prevalence of foot lesions by type of milking system in dairy cows examined during regular hoof-trimming sessions between 2015 and 2018 in Québec dairy herds. A secondary objective was to describe the effect of day-to-day variation, cow, and herd characteristics on the prevalence of foot lesions. Data included 52,427 observations (on a cow during a specific trimming session) performed on 28,470 cows (≥2 yr old) from 355 herds. Only observations from trimming sessions in which ≥90% of the lactating herd was trimmed were considered. Lesions were recorded at the hoof level by 17 trained hoof trimmers between March 23, 2015, and July 10, 2018, using a computerized recording system. Hoof-level information was then matched with cow information and centralized at the Eastern Canada Dairy Herd Improvement. Foot lesions were classified into 6 categories: infectious, white line disease, heel erosion, ulcers, hemorrhages, and any type of foot lesions. Prevalence of each outcome was quantified using the marginal predicted mean probability estimated from a null generalized linear mixed model with a logit link, and accounted for clustering of observations by cow and by herd. Variance was partitioned to assess the variation in the probability of the outcomes attributable to each level of the data structure (day of exam, cow, and herd). Prevalence of a given foot lesion as function of milking system and of various explanatory variables (mean herd size, herd average daily production, breed of the cow, age of the cow at trimming, and year of the visit) was then estimated using a generalized linear mixed model. At least 1 foot lesion was observed in 29% of cows examined during regular trimming sessions in Québec from 2015 to 2018. Prevalence for any type of lesion was 27% for pipeline, 38% for robotic milking, and 41% for milking parlors. The highest prevalence of infectious lesions (mainly digital dermatitis) was observed in milking parlors and robotic systems, while the most prevalent lesions in pipeline were hemorrhages. Herd-level factors explained most of the disease probability for infectious diseases, heel erosion, and hemorrhages. Therefore, control of these diseases should be based on applying best herd-management practices. On the other hand, probabilities of white line disease and sole ulcers were mainly determined by cow-level characteristics.

In the province of Quebec, Canada, a new regulation restricting usage of antimicrobials of very high importance for human health (Health Canada: category 1 antimicrobials) in production animals is effective since February 2019. The objective of this study was to estimate changes in AM sales in dairy herds after the implementation of the regulation. Therefore, invoice data were extracted from veterinary software, Vet-Expert, used by most dairy veterinarians in the province of Quebec, and antimicrobial quantities were transformed in Canadian defined course doses for cattle (DCDbovCA). The sum of antimicrobials sales monthly in each herd was estimated in DCDbovCA from June 2016 to May 2020. To evaluate the herd-level change in AM sales and the impact of different factors, the number of DCDbovCA by herd from June 2017 to May 2018 (pre-regulation period) were compared with those of June 2019 to May 2020 (post-regulation period). Total category 1 AM sales of 3,569 Quebec's herds went from a range of 14,258 to 21,528 DCDbovCA/month to a range of 1,494 to 4,707 DCDbovCA/month after the implementation of the new regulation. Moreover, using data from 3,337 herds, we estimated a mean (95% confidence interval) reduction in 19 DCDbovCA/herd-year (14.8, 24.2), while the pre-regulation herd-level category 1 AM sales was 26 DCDbovCA/herd-year. This reduction was achieved without evidence of an increase in other antimicrobials. Finally, the veterinary facility associated with the herd was an important determinant of the herd-level reduction in category 1 antimicrobials. This study was the first to quantify a significant reduction in category 1 AM sales following the implementation of a restrictive regulation in dairy production in Canada. These results demonstrate that such an approach is effective to reduce the sales of a specific category of antimicrobial in animal production.

Mechanochemistry enables rapid access to boron imidazolate frameworks (BIFs), including ultralight materials based on Li and Cu( i ) nodes, as well as new, previously unexplored systems based on Ag( i ) nodes.

To tackle antimicrobial resistance (AMR), one of the major health threats of this century, the World Health Organization (WHO) endorsed a global action plan in 2015. This plan calls countries to develop national actions to address AMR. The province of Québec, Canada, adopted a new regulation on the 25 th of February 2019, to limit the use in food animals of antimicrobials of very high importance in human medicine. We aimed to establish the impact of this regulation by comparing the AMR situation in dairy cattle in Québec ~2 years before and 2 years after its introduction. We sampled calves, cows, and the manure pit in 87 farms. Generic and putative ESBL/AmpC E. coli were tested for susceptibility to 20 antimicrobials. Logistic regression was used to investigate whether the probability of antimicrobial resistance differed between isolates obtained from the pre and post regulation periods by sample type (calves, cows, manure pit) and in general. To identify AMR genes dissemination mechanisms, we sequenced the whole genome of 15 generic isolates. In the generic collection, at the herd level, the proportion of multidrug resistant (MDR) isolates, decreased significantly from 83 to 71% ( p = 0.05). Folate inhibitor and aminoglycoside resistances demonstrated a significant decrease. However, when analyzed by sample type (calves, cows, manure pit), we did not observe a significant AMR decrease in any of these categories. In the ESBL/AmpC collection, we did not detect any significant difference between the two periods. Also, the general resistance gene profile was similar pre and post regulation. We identified both clonal and plasmidic dissemination of resistance genes. In conclusion, as early as 2 years post regulation implementation, we observed a significant decrease in MDR in the dairy industry in Quebec in the generic E. coli collection with folate inhibitor and aminoglycoside resistances showing the most significant decrease. No other significant decreases were yet observed.

ABSTRACT Escherichia coli is a common environmental pathogen associated with clinical mastitis (CM) in dairy cattle. There is an interest in optimizing the udder microbiome to increase the resistance of dairy cattle to E. coli CM; however, the details of which members of the healthy udder microbiome may play a role in antagonizing E. coli are unknown. In this study, we characterized the bacterial community composition in raw milk collected from quarters of lactating Holstein dairy cows that developed E. coli CM during lactation, including milk from both healthy and diseased quarters ( n = 1,172). The milk microbiome from infected quarters was compared before, during, and after CM. A combination of 16S rRNA gene amplicon and metagenomic sequencing was used generate data sets with a high level of both depth and breadth. The microbial diversity present in raw milk significantly decreased in quarters experiencing E. coli CM, indicating that E. coli displaces other members of the microbiome. However, the diversity recovered very rapidly after infection. Two genera, Staphylococcus and Aerococcus , and the family Oscillospiraceae were significantly more abundant in healthy quarters with low inflammation. Species of these genera, Staphylococcus auricularis, Staphylococcus haemolyticus, and Aerocussus urinaeequi , were identified by metagenomics. Thus, these species are of interest for optimizing the microbiome to discourage E. coli colonization without triggering inflammation. IMPORTANCE In this study, we show that E. coli outcompetes and displaces several members of the udder microbiome during CM, but that microbial diversity recovers post-infection. In milk from quarters which remained healthy, the community composition was often highly dominated by S. auricularis, S. haemolyticus, A. urinaeequi, and S. marcescens without increases in somatic cell count (SCC). Community dominance by these organisms, without inflammation, could indicate that these species might have potential as prophylactic probiotics which could contribute to colonization resistance and prevent future instances of E. coli CM.

Salmonella species are bacteria that are a major source of foodborne disease through contamination of a diversity of foods, including meat, eggs, fruits, nuts, and vegetables. More than 2,600 different Salmonella enterica serovars have been identified, and only a few of them are associated with illness in humans. Despite the fact that they are genetically closely related, there is enormous variation in the virulence of different isolates of Salmonella enterica . Identification of foodborne pathogens is a lengthy process based on microbiological, biochemical, and immunological methods. Here, we worked toward new ways of integrating whole-genome sequencing (WGS) approaches into food safety practices. We used WGS to build associations between virulence and genetic diversity within 83 Salmonella isolates representing 77 different Salmonella serovars. Our work demonstrates the potential of combining a genomics approach and virulence tests to improve the diagnostics and assess risk of human illness associated with specific Salmonella isolates.