加拿大公共卫生署

Antimicrobial resistance (AMR) is a growing global public health concern affecting animals, humans, and the environment. Given its ubiquity, Escherichia coli may play a key role in the dissemination of AMR across these domains. Peri-urban regions where urban and rural systems intersect present unique challenges for controlling AMR. Despite this, limited data are available on AMR dissemination across the One Health continuum in peri-urban settings such as the Fraser Valley region of Canada. This study adopted a One Health approach to assess associations in AMR traits between E. coli from dairy production systems, nearby natural environments, and peri-urban communities within the same geographic location and timeframe. Over 1,000 isolates were recovered, and 421 were whole-genome sequenced to determine the presence of antimicrobial resistance genes (ARGs), plasmids, and virulence genes and to assess genomic relatedness. Findings revealed that AMR was not widespread: 17.8% of isolates carried at least one ARG, 10.2% were classified as multidrug-resistant, and 9.5% carried beta-lactamase genes. Phylogenomic analysis revealed high genomic diversity, with isolates belonging to 174 different sequence types (STs), including clinically important ST131 and ST10. Pairwise single-nucleotide polymorphism (SNP) comparisons identified 207 isolate pairs differing by ≤100 SNPs, indicating early-stage cross-domain movement of AMR. Overall, the findings from this study show that the prevalence of AMR E. coli is low, but there is evidence of transmission between animals and the environment, highlighting the importance of proactive, integrated surveillance and mitigation strategies to reduce the risk of future AMR dissemination across the One Health continuum. IMPORTANCE:Antimicrobial resistance (AMR) is a global public health concern that spans all three One Health domains (humans, animals, and the environment). Escherichia coli is present in humans, animals, and environmental sources-its ubiquity makes it an ideal organism to study AMR hotspots and transmission pathways across the One Health continuum. While surveillance of AMR in agricultural settings is increasing globally, little is known about transmission pathways in peri-urban agriculture areas where there is a high density of livestock farming in close proximity to residential communities. To identify potential AMR hotspots and transmission routes, this study investigated the occurrence and genomic relatedness of generic E. coli in the Fraser Valley region of British Columbia, a highly diverse agricultural region in western Canada. Our findings expand current knowledge by suggesting that early-stage transmission of AMR is occurring between the human, animal, and environmental sectors of the One Health triad, highlighting areas for improved resistance mitigation to prevent widespread dissemination.

The advent of metabarcoding has greatly advanced our understanding of nematode ecology by overcoming many limitations associated with traditional morphology-based methods. The NF1-18Sr2b (NF1) is the standard and widely used primer pair to assess nematode communities. However, this primer also presents challenges, especially when applied to DNA extracted directly from soil, where it has been shown to underestimate species richness. Consequently, soil DNA extraction (SE) has been viewed as a less attractive option for metabarcoding studies. To explore whether nematode DNA extraction (NE) can serve as a viable option for metabarcoding studies, we compared two degenerate primer pairs, NemF-18Sr2b (NemF) and NemFopt-18Sr2bRopt (NemFopt) to NF1. The study used two DNA sources: NE, and SE derived from 10 g and 1.25 g of dry agricultural soils. Our findings indicate that the NemF and NemFopt primers yielded higher taxonomic resolution and species richness in both SE and NE compared to NF1. Specifically, NF1 detected only 2-4% of nematode sequences in SE and 69% in NE, whereas NemFopt detected the highest proportion, with 100% of nematode sequences in NE and >70% in SE. Although none of the primers amplified all taxa, NF1 was associated with higher undetected taxa. NemFopt in the 10 g SE identified nematode assemblages comparable to those from NE, suggesting that SE can effectively capture nematode communities similar to NE. Nematode community profiles and ecological indices were stable across soil DNA input volumes and DNA sources. Maturity index and enrichment index did not differ significantly between NE and SE. Community similarity across extraction methods varied with primer choice, with NemFopt showing the greatest consistency. Although this study was limited to two soil types, two field sites, and three primer sets, our results suggest that increasing primer specificity can reduce the amount of soil required for metabarcoding and make SE a viable option. Moreover, primer choice, soil type, and DNA source can significantly affect nematode diversity estimates and ecological interpretations, highlighting the need for primer standardization in nematode metabarcoding studies.

Introduction: Detection of pathogens associated with bovine respiratory disease (BRD) typically involves several laboratory tools, with results limited to a defined list of targets. This study adapted a previously reported method for metagenomic sequencing of nasal swabs to describe sequencing data from BRD associated viruses. Changes in virus composition were identified between arrival to a feedlot and 14 days on feed (DOF). These data were also assessed for the simultaneous characterization of bacteria and antimicrobial resistance genes (ARGs). Methods: Nasal swabs were obtained from fall-placed calves (FPC) and yearlings (YRL) from western Canadian commercial feedlots. Evidence of respiratory viruses were identified by sampling 380 animals during processing on arrival to the feedlot and again after 14 DOF using Nanopore metagenomic sequencing. Results: Twenty-one distinct viruses from 12 viral families were identified, with multiple viruses detected in most samples. In FPC arrival samples, the most common BRD associated viruses were bovine rhinitis B virus (BRBV; 46%), bovine coronavirus (BCoV; 32%), influenza D virus (IDV; 17%), bovine respiratory syncytial virus (BRSV; 8.5%), and bovine parainfluenza virus 3 (BPIV-3; 4.2%). The prevalences of bovine herpesvirus type 1 (BoHV-1; 2.7%), BPIV-3 (12%), BRSV (26%), and IDV (51%) were higher in 14 DOF samples compared to arrival samples (p < 0.05). Bovine viral diarrhea virus 1 (BVDV-1) and 2 (BVDV-2) were rarely detected at either time. The most prevalent viruses detected in YRL arrival samples were BRBV (42%), BRSV (39%), BPIV-3 (20%), IDV (16%), BCoV (12%), and BVDV-2 (7.5%). The prevalences of BRSV (60%), BPIV-3 (39%), and BVDV-2 (17%) were higher in 14 DOF samples than arrival samples (p < 0.05). BRSV (OR 7.0, 1.7-29) and BPIV-3 (OR 5.7, 1.5-21) were more likely to be detected in arrival samples from YRL than FPC (p = 0.01). In 14 DOF samples, BPIV-3 (OR 4.9, 1.3-19, p = 0.02) and BVDV-2 (OR 13, 2.0-83, p = 0.01) were identified more frequently in YRL than FPC. These data allowed the identification of respiratory bacteria and 33 ARGs in parallel with assessment of the viral components. The most prevalent bacteria detected in FPC at arrival were Mannheimia haemolytica (35%), Histophilus somni (35%) and Pasteurella multocida (23%). Detection of M. haemolytica increased at 14 DOF (p = 0.02), while P. multocida detection decreased (p = 0.03). At both arrival and 14 DOF in YRL, M. haemolytica was the most prevalent bacterium, followed by P. multocida and H. somni with no significant differences between arrival and 14 DOF samples. ARGs were detected more frequently in the 14 DOF samples than at arrival for both FPC (p = 0.03) and YRL (p = 0.01). The most commonly detected ARGs were associated with resistance to lincosamides and aminoglycosides; however, ARGs associated with other antimicrobials used in cattle including tetracyclines were also identified. Discussion: Changes in the prevalence of BRD associated viruses early in the feeding period reflect transmission and the potential risk of developing the disease. Frequent detection of BCoV, BRSV, and BPIV-3 in newly arrived feedlot cattle suggests the need for improved vaccination before shipping or limitations in existing commercial vaccine preparations.

Antimicrobial resistance (AMR) challenges the effective treatment of bovine respiratory disease (BRD). We evaluated the performance of a recombinase polymerase amplification (RPA) assay, a rapid, isothermal nucleic-acid amplification method, compared with bacterial culture (BC), antimicrobial susceptibility testing (AST), and real-time PCR (rtPCR) testing. We cultured deep nasopharyngeal swabs collected from 800 beef calves within 36 d on feed and at first treatment for BRD for Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni, and screened for these species and Mycoplasmopsis bovis using RPA (M. haemolytica serotypes 1 and 6 only) and rtPCR (M. bovis only). We then tested samples that were RPA-positive for Pasteurellaceae for integrative and conjugative element (ICE) variants containing tetH (ICEtnpA, ICEebrB) and macrolide antimicrobial-resistance genes (ARGs; msrE-mphE, erm42). Bayesian latent class models estimated the clinical sensitivity of BC to be higher than RPA for Pasteurellaceae detection. Both methods were highly specific. RPA sensitivity for M. bovis detection was comparable to rtPCR, but RPA specificity was higher. RPA specificity for detection of macrolide resistance was lower (93.5%) than BC-AST (99.9%), reflecting the identification of ARGs by RPA in non-target bacteria. However, the sensitivity of both tests was low (BC-AST: 20.5%; RPA: 13.3%). Limited RPA sensitivity for Pasteurellaceae identification constrained its downstream performance for detecting ARGs. With our large-scale study, we demonstrated that RPA could detect key BRD-associated pathogens and AMR determinants directly from respiratory samples. Although our RPA results were not sufficient to inform AMU treatment strategies, RPA testing could prove valuable for addressing focused investigations with rapid turnaround.

BACKGROUND:Mobility, defined as movement in all its forms, is a hallmark of healthy ageing. As wearable technologies become increasingly integrated into population health surveillance and ageing research, the absence of standardised terminology, measurement protocols and reporting practices presents a major barrier to progress. This consensus exercise aimed to establish minimum standards for measuring mobility with wearable technology in ageing populations and set priorities for future research in the field. METHODS:A two-day, in-person consensus meeting was convened with 24 international experts in ageing, mobility and digital health. Using a modified nominal group technique facilitated by a trained moderator, participants engaged in structured small-group brainstorming, followed by iterative large-group discussions. Consensus was achieved through anonymised digital voting on proposed measures, principles and priorities. FINDINGS:Consensus (≥80% agreement) was reached on 20 core device-derived mobility measures and 30 guiding principles for the optimal use of wearable technology in older populations. Experts also identified and ranked 16 priority areas for future research, with the top five including: (i) longitudinal studies and data collection, (ii) digital biomarkers and health outcomes, (iii) contextual data capture, (iv) algorithm development and validation and (v) integration with healthcare systems. INTERPRETATIONS:These consensus-based standards provide a foundational framework for the consistent and transparent use of wearable devices in ageing research and practice. They can inform the development of regulations and guidelines, support harmonisation across studies and chart a path for future research to enhance the utility and impact of wearable technologies in ageing populations.