Canadian journal of microbiology最新文献

{"title":"Crossing the streams: improving data quality and integration across the One Health genomics continuum with data standards and implementation strategies.","authors":"Emma J Griffiths, Emil Jurga, Gabriel Wajnberg, Julie A Shay, Rhiannon Cameron, Charlie Barclay, Anoosha Sehar, Damion Dooley, Nithu Sara John, Andrew Scott, Lisa A Johnson, James Robertson, Justin Schonfeld, D Patrick Bastedo, Joshua Tang, Xianhua Yin, Attiq Rehman, Rhiannon L Wallace, Krysty Thomas, Shannon H C Eagle, Tim McAllister, Moussa S Diarra, John H E Nash, Ed Topp, Gary Van Domselaar, Eduardo Taboada, Sandeep Tamber, Tony Kess, Jordyn Broadbent, Dominic Poulin-Laprade, Derek D N Smith, Richard Reid-Smith, Rahat Zaheer, Chad R Laing, Catherine D Carrillo, William W L Hsiao","doi":"10.1139/cjm-2024-0203","DOIUrl":"10.1139/cjm-2024-0203","url":null,"abstract":"<p><p>The Canadian Genomics Research and Development Initiative for Antimicrobial Resistance (GRDI-AMR) uses a genomics-based approach to understand how health care, food production and the environment contribute to the development of antimicrobial resistance. Integrating genomics contextual data streams across the One Health continuum is challenging because of the diversity in data scope, content and structure. To better enable data harmonization for analyses, a contextual data standard was developed. However, development of standards does not guarantee their use. Implementation strategies are critical for putting standards into practice. This work focuses on the development of implementation strategies to better operationalize data standards across the Canadian federal genomics ecosystem. Results include improved understanding of complex data models that can create challenges for existing systems. Technical implementation strategies included spreadsheet-based solutions, new exchange formats, and direct standards integration into new databases. Data curation exercises highlighted common data collection and sharing issues, which informed improved practices and evaluation procedures. These new practices are contributing to improved data quality and sharing within the GRDI-AMR consortium as evidenced by publicly available datasets. The implementation strategies and lessons learned described in this work are generalizable for other standards and can be applied more broadly within other initiatives.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-14"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of viable <i>Enterobacteriaceae</i> and <i>Enterococcus</i> spp. across the agro-ecosystem of an antibiotic-free swine farm.","authors":"Alexandra Langlois, Antony T Vincent, Renée M Petri, Karoline Lauzon, Dominic Poulin-Laprade","doi":"10.1139/cjm-2024-0173","DOIUrl":"10.1139/cjm-2024-0173","url":null,"abstract":"<p><p>Agricultural practices, specifically the use of antibiotics and other biocides, have repercussions on human, animal, and plant health. The aim of this study was to evaluate the levels of <i>Enterobacteriaceae</i> and <i>Enterococcus</i>, as antibiotic-resistant marker bacteria, in various matrices across the agro-ecosystem of an antibiotic-free swine farm in Quebec (Canada), namely pig feed, feces, manure, agricultural soil, water and sediment from a crossing stream, and soil from nearby forests. Samples were collected in fall 2022, spring and fall 2023, and spring 2024. All samples were subjected to counts of total, cefotaxime-, and ciprofloxacin-resistant <i>Enterobacteriaceae</i> as well as total and vancomycin-resistant <i>Enterococcus</i> spp. The frequency of total and cefotaxime-resistant <i>Enterobacteriaceae</i> along with the vancomycin-resistant <i>Enterococcus</i> decreased with age in pig feces, from weaning to the end of the fattening period. High proportions of the <i>Enterobacteriaceae</i> recovered from feces and environmental samples were resistant to cefotaxime. Application of manure on fields contributed a significant input of <i>Enterococcus</i>, but those resistant to vancomycin were under the detection limit. This study shows the prevalence of antibiotic-resistant bacteria in a farm agro-ecosystem even without the administration of antibiotics to the animals and highlights the complexity of components influencing antimicrobial resistance in the environment.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-14"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"11th International Symposium on Avian Influenza.","authors":"Andrew S Lang, Michelle Wille","doi":"10.1139/cjm-2025-0196","DOIUrl":"https://doi.org/10.1139/cjm-2025-0196","url":null,"abstract":"","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":"71 ","pages":"1-3"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial biodiversity of agricultural surface waters in Ontario, Canada.","authors":"Izhar U H Khan, Yutao Wang, Tiequan Zhang, Keri Malanchuk, Shanwei Xu, Sophie Crevecoeur, Josh Wang, Arthur Zastepa, Xiaoji Liu","doi":"10.1139/cjm-2025-0015","DOIUrl":"https://doi.org/10.1139/cjm-2025-0015","url":null,"abstract":"<p><p>Understanding the microbial diversity is the first step to monitor the microbial quality of agricultural surface waters. Here we report a study comparing the microbial composition and diversities in agricultural surface waters in Ontario, Canada, including the streams adjacent to dairy cattle production in eastern Ontario and the field runoffs from the manure-impacted experimental farm of south-western Ontario. We also studied the quality of the surface water in the western basin of Lake Erie during a harmful algal bloom (cHAB). In eastern Ontario, we found significantly lower (<i>P</i> < 0.01) abundance of Proteobacteria and Burkholderiales in the streams adjacent to dairy production than the non-agriculture site. Bacteroidetes was more abundant (<i>P</i> < 0.0001) in medium/high order streams and agriculture/urban mixed site. Seasonal peaks of <i>Flavobacterium</i> were observed in low order streams but the trend was not in medium/high order streams. In south-western Ontario, the dominant bacterial taxa in field runoffs was <i>Pseudomonas</i>, regardless of manure types. We also discovered that the elevated total dissolved nitrogen, total dissolved phosphorus and chlorophyll a associated with the cHAB zone in Lake Erie was further away rather from the agricultural sites. In conclusion, our studies identified unique microbiome patterns associated with agricultural surface waters in Ontario.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":"71 ","pages":"1-9"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic and genomic insights of <i>Flavobacterium</i> diversity in Quebec's fish farms.","authors":"Vincent Gélinas, Valérie E Paquet, Maude F Paquet, Antony T Vincent, Steve J Charette","doi":"10.1139/cjm-2025-0076","DOIUrl":"10.1139/cjm-2025-0076","url":null,"abstract":"<p><p>The genus <i>Flavobacterium</i> constitutes a vast pool of microorganisms living in multiple environmental niches including fish pathogens and species in the fish microbiome. Veterinary reports have identified flavobacteria in fish from Quebec's fish farms, confirming their association with infections. However, these reports have not conducted in-depth characterization, and the diversity of nonpathogenic flavobacteria in Quebec remains unknown. This study is the first step in assessing the diversity of <i>Flavobacterium</i> in Quebec's fish farms, without focusing solely on pathogenic strains. Seventeen isolates were collected from different fish farms, from either the water or fish. Microbial species identification was performed using PCR genotyping of the <i>gyrB</i> gene, whole-genome sequencing, and phylogenetic analysis. Antimicrobial susceptibility tests for tetracycline and florfenicol, the two most commonly used antibiotics in Quebec aquaculture, along with predictive tools, were employed to assess resistance. This study revealed potential new species among the isolates. No known pathogenic species were detected, and all 17 isolates clustered within CIIIb or CIIIc, recently described phylogenetic clades of <i>Flavobacterium</i> found in various environments, and the majority showed resistance to antibiotics. This study highlights the expanding diversity of <i>Flavobacterium</i>, particularly among species associated with fish, and underscores the need for further research in Quebec.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-9"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dr. Robert Murray: strong roots in Canadian microbiology-strong global leadership and vision.","authors":"Susan F Koval, Cezar M Khursigara","doi":"10.1139/cjm-2025-0285","DOIUrl":"https://doi.org/10.1139/cjm-2025-0285","url":null,"abstract":"","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":"71 ","pages":"1-3"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145585866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Penicillium sanguifluum</i> (<i>Penicillium</i> section <i>Citrina</i>) as a source of dehydrocurvularin and its antifungal and antibacterial properties.","authors":"Aamer Kurdi, Harman Gill, Taylor MacLeod, John L Sorensen, Georg Hausner, Ayush Kumar","doi":"10.1139/cjm-2025-0048","DOIUrl":"10.1139/cjm-2025-0048","url":null,"abstract":"<p><p>Antimicrobial resistance has a negative impact on people's health and the economy. New resistance mechanisms are emerging, making the treatment of infections very challenging. Fungi are well known for their production of secondary metabolites during active cell growth. In this study, a strain of <i>Penicillium sanguifluum</i> (111-12) was isolated from Manitoba soil and investigated for antimicrobial properties of fungal secondary metabolites against pathogenic bacteria, and two fungal plant pathogens that are known for causing Dutch elm diseases and chestnut blight disease. <i>Penicillium sanguifluum</i> (111-12) produced dehydrocurvularin (C1) and 11-hydroxycurvularin (C2). C1 and C2 were examined for their antimicrobial properties and these compounds were combined with various antibiotics to evaluate their potentiation (adjuvant) properties. Promising results were obtained for C1 that decreased the minimum inhibitory concentrations of cefepime, ceftazidime, tobramycin, and amikacin against a clinical multidrug resistant strain of <i>Pseudomonas aeruginosa</i> (PA82). In addition, C1 and C2 showed no impact on the <i>Galleria mellonella</i> model regarding toxicity.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-14"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145387098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Survey of fungal endophytes in barley under Fusarium head blight infection.","authors":"Denice Embrador, Zoe Quill, James R Tucker, Keval Shah, Ana Badea, Champa Wijekoon","doi":"10.1139/cjm-2024-0137","DOIUrl":"10.1139/cjm-2024-0137","url":null,"abstract":"<p><p>Fusarium head blight (FHB) is a devastating fungal disease caused by <i>Fusarium graminearum</i>, which affects barley (<i>Hordeum vulgare</i> L.) and other small cereal grains. Fungal endophytes are microorganisms that reside inside tissues and considered that they may have been involved in various roles of the plants. This study involved the comparison of fungal endophytes between \"non-infected/clean\" and \"FHB-infected\" barley genotypes in various tissues collected at different plant developmental stages and were grown under different conditions (i.e., greenhouse, research field, and FHB-field nursery). We hypothesized that fungal endophytes diversity and abundance may differ between plant tissues in various barley genotypes that were non-infected and FHB-infected. The 18S-internal transcribed spacer sequencing analysis revealed a greater number of fungal operational taxonomic units (OTUs) and endophyte species in FHB-infected barley compared to clean barley. A one-way ANOVA and Tukey's pairwise comparison test (<i>p</i> ≤ 0.05) were performed to test significant differences. Higher seed endophyte diversity was found in FHB-infected (120 OTUs) compared to non-infected (113 OTUs) harvested in 2021. The increase in diversity of endophytes that contributes to different roles in plant protection and defense, such as biocontrol agents, may prevent the growth of <i>Fusarium</i> species and decrease FHB-infection.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-16"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143784558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A β-amino-ketone that disrupts the fungal plasma membrane exhibits potent activity against pathogenic <i>Trichophyton</i> species.","authors":"Jéssica Cristina Polveiro Campos, Diego Batista Carneiro de Oliveira, Bruna da Silva Souza, Lucas Felipe de Oliveira, Ezequias Pessoa de Siqueira, Markus Kohlhoff, Anderson Assunção Andrade","doi":"10.1139/cjm-2025-0009","DOIUrl":"10.1139/cjm-2025-0009","url":null,"abstract":"<p><p>Superficial fungal infections, mainly caused by dermatophytes, are a global public health issue. We evaluated the antifungal activity of six β-amino-ketones against <i>Trichophyton rubrum</i>, a leading agent of superficial mycoses. Among them, 3-(morpholin-4-yl)-1-phenylpropan-1-one (<b>AB1</b>) showed the most potent effect, with a minimum inhibitory concentration (MIC) of 7.81 µg/mL against the <i>T. rubrum</i> reference strain and fungicidal activity against clinical isolates, as demonstrated by minimum fungicidal concentration assays. <b>AB1</b> was effective against both conidia and hyphae of <i>T. rubrum</i>, while showing limited activity against <i>Candida albicans</i> and the bacteria <i>Escherichia coli</i> and <i>Staphylococcus aureus</i>. Mechanistic studies suggest <b>AB1</b> targets the fungal plasma membrane, possibly via ergosterol interactions, supported by increased MICs in ergosterol-rich conditions and membrane integrity assays. Confocal microscopy revealed morphological alterations in <b>AB1</b>-treated hyphae, indicative of membrane damage. Transmission electron microscopy confirmed cytoplasmic disorganization and membrane disruption at subinhibitory concentrations. Toxicological assays showed moderate cytotoxicity in human fibroblasts (IC₅₀ = 37.75 µg/mL) and no toxicity in <i>Galleria mellonella</i> larvae at high doses. These findings highlight <b>AB1</b> as a promising antifungal candidate against <i>Trichophyton</i> spp., with the potential benefit of reduced impact on the host microbiota compared to broad-spectrum antimicrobials.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-11"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144157006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Requirements and considerations for effective implementation of integrated One Health antimicrobial resistance research.","authors":"Dominic Poulin-Laprade, Jordyn Broadbent, Damien Biot-Pelletier, Susanne Kraemer, Emma J Griffiths, Ayush Kumar, Xian-Zhi Li, Catherine D Carrillo, Rahat Zaheer, Tim A McAllister, Sigrun Kullik, Ernesto Liebana, Nicole Ricker, Alexandra Langlois, Richard J Reid-Smith, Sébastien P Faucher, Gabriela Flores-Vargas, Emilie Bédard, J Kimberley Summers, Veronica Jarocki, Thanaporn Thongthum, Carolee A Carson","doi":"10.1139/cjm-2024-0194","DOIUrl":"10.1139/cjm-2024-0194","url":null,"abstract":"<p><p>The One Health (OH) approach recognizes the interconnectedness of the health of people, animals, plants/crops and ecosystems, and is central to addressing antimicrobial resistance (AMR). The 7th Environmental Dimension of Antimicrobial Resistance Conference (EDAR7), held in Montreal in May 2024, exemplified this approach by convening international experts and stakeholders to discuss AMR research and policy progress. EDAR7 workshop #8 focused on (1) barriers to establishing effective OH AMR research programs, (2) gaps in OH AMR research priorities, and (3) potential solutions/approaches or \"tools\" to ensure programs develop in accordance with OH principles and generate insightful data that maximizes limited resources. Key workshop outcomes included identifying critical principles for OH AMR research programs and highlighting the pivotal role of sustainable data management strategies. Additionally, the importance of considering AMR policy and risk assessment needs when planning and designing research was emphasized. Discussions explored specific tools and approaches that support the standardized and harmonized collection and analysis of data, and associated challenges of integrating genomics data into current risk assessments and models. Synthesis of the workshop's discussions outlined critical considerations that interdisciplinary OH AMR research programs and networks should prioritize to enhance the impact of their outputs.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-17"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144483235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}