Canadian journal of microbiology最新文献

{"title":"<i>Candida albicans</i>: a historical overview of investigations into an important human pathogen.","authors":"Manjari Shrivastava, Malcolm Whiteway","doi":"10.1139/cjm-2025-0036","DOIUrl":"https://doi.org/10.1139/cjm-2025-0036","url":null,"abstract":"<p><p>In recent decades, the study of the opportunistic pathogenic fungus, <i>Candida albicans</i>, has been revolutionized by genomics, transforming our understanding of its molecular biology, pathogenicity, and modes of drug resistance. In this review, our effort is to trace the historical development of <i>C. albicans</i> research, from early clinical observations to modern high-throughput genomic techniques. Advances in molecular biology, transcriptomics, and genome editing, including CRISPR-Cas9, have had a significant impact on the genetic tools available for studying this pathogen. The impact of whole-genome sequencing, functional genomics, and single-cell transcriptomics on the study of <i>C. albicans</i>, alongside the role of fungal population genomics in tracking evolutionary adaptations, have resulted in key insights. Here we discuss the ongoing challenge of antifungal resistance and the implications of new technologies in combating invasive candidiasis. As we move into a new era of precision mycology, integrating multi-omics approaches will further enhance our ability to understand and control <i>C. albicans</i> infections.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":"71 ","pages":"1-21"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301137","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 pilot study on the effects of in-feed probiotic <i>Lactobacillus rhamnosus</i> ATCC 53103 (LGG) on vaccinated Atlantic salmon (<i>Salmo salar</i>): microbiomes and <i>Aeromonas salmonicida</i> challenge resilience.","authors":"Natalia Lorenc, Steven Leadbeater, Josh Wang, Jennifer Ronholm, Xiaoji Liu","doi":"10.1139/cjm-2024-0130","DOIUrl":"10.1139/cjm-2024-0130","url":null,"abstract":"<p><p>The use of probiotics is an alternative approach to mitigate the proliferation of antimicrobial resistance in aquaculture. In our study, we examined the effects of <i>Lactobacillus rhamnosus</i> GG (ATCC 53103, LGG) delivered in-feed on the weight, length, skin mucus, and faecal microbiomes of Atlantic salmon. We also challenged the salmon with <i>Aeromonas salmonicida</i> 2004-05MF26 (Asal2004) and assessed the mortality. Our results showed no significant change (<i>P</i> > 0.05) in weight or length of Atlantic salmon or their resilience to Asal2004 infection after LGG feeding. Infection changed significantly the skin mucus and faecal microbiomes: <i>Clostridium sensu stricto</i> increased from 3.14% to 9.20% in skin mucus and 1.39% to 3.74% in faeces (<i>P</i> < 0.05). <i>Aeromonas</i> increased from 0.02% to 0.60% in faeces (<i>P</i> < 0.05). <i>Photobacterium</i> increased from not detected (0%) to 52.16% (<i>P</i> < 0.01) and <i>Aliivibrio</i> decreased from 67.21% to 0.71% in faeces (<i>P</i> < 0.01). After infection, <i>Lactococcus</i> (9.93%) and <i>Lactobacillus</i> (2.11%) in skin mucus of the LGG group were significantly higher (<i>P</i> < 0.05) than in the skin mucus from the rest of the groups (4.14% and 1.08%, respectively). In conclusion, LGG feeding did not further increase the resilience of vaccinated Atlantic salmon. Asal2004 infection had much greater impact on skin mucus and faecal microbiomes than LGG feeding.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-10"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000693","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":"Variation in plasmid conjugation among nontyphoidal <i>Salmonella enterica</i> serovars.","authors":"Anna Laidlaw, Madeleine Blondin-Brosseau, Julie A Shay, Forest Dussault, Mary Rao, Nicholas Petronella, Sandeep Tamber","doi":"10.1139/cjm-2024-0164","DOIUrl":"10.1139/cjm-2024-0164","url":null,"abstract":"<p><p>Conjugation is a complex phenomenon involving multiple plasmid, bacterial, and environmental factors. Here we describe an IncI1 plasmid encoding multidrug antibiotic resistance to aminoglycosides, sulfonamides, and third-generation cephalosporins. This plasmid is widespread geographically among animal, human, and environmental sectors. We present data on the transmissibility of this plasmid from <i>Salmonella</i> <i>enterica</i> ser. Kentucky into 40 strains of <i>S. enterica</i> (10 strains each from serovars Enteritidis, Heidelberg, Infantis, and Typhimurium). Thirty seven out of 40 strains were able to take up the plasmid. Rates of conjugation were variable between strains ranging from 10^-8 to 10^-4. Overall, serovars Enteritidis and Typhimurium demonstrated the highest rates of conjugation, followed by Heidelberg, and then Infantis. No relationships were observed between the recipient cell surface and rate of conjugation. Recipient cell numbers correlated positively with conjugation rate and strains with high conjugation rates had marginally but significantly higher growth parameters compared to strains that took up the plasmid at lower frequencies. Environmental conditions known to impact cell growth, such as temperature, nutrient availability, and the presence of antibiotics, had a modulating effect on conjugation. Collectively, these results will further understanding of plasmid transmission dynamics in <i>Salmonella</i>, which is a critical first step towards the development of mitigation strategies.</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":"142853058","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":"Engineering conjugative plasmids for inducible horizontal DNA transfer.","authors":"Tahani Jaafar, Emily Carvalhais, Arina Shrestha, Ryan R Cochrane, Jordyn S Meaney, Stephanie L Brumwell, Samir Hamadache, Vida Nasrollahi, Bogumil J Karas","doi":"10.1139/cjm-2024-0241","DOIUrl":"10.1139/cjm-2024-0241","url":null,"abstract":"<p><p>Rapidly developing microbial resistance to existing antimicrobials poses a growing threat to public health and global food security. Current chemical-based treatments target cells by inhibiting growth or metabolic function, but their effectiveness is diminishing. To address the growing antimicrobial resistance crisis, there is an urgent need for innovative therapies. Conjugative plasmids, a natural mechanism of horizontal gene transfer in bacteria, have been repurposed to deliver toxic genetic cargo to recipient cells, showing promise as next-generation antimicrobial agents. However, the ecological risks posed by unintended gene transfer require robust biocontainment strategies. In this study, we developed inducible conjugative plasmids to solve these challenges. Utilizing an arabinose-inducible promoter, we evaluated 13 plasmids with single essential gene deletions, identifying trbC and trbF as strong candidates for stringent regulation. These plasmids demonstrated inducibility in both <i>cis</i> and <i>trans</i> configurations, with induction resulting in up to a 5-log increase in conjugation efficiency compared to uninduced conditions. Although challenges such as reduced conjugation efficiency and promoter leakiness persist, this work establishes a foundation for the controlled transfer of plasmids, paving the way for safer and more effective antimicrobial technologies.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-9"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762954","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":"From patterns to prediction: machine learning and antifungal resistance biomarker discovery.","authors":"Veronica Thorn, Jianping Xu","doi":"10.1139/cjm-2024-0248","DOIUrl":"https://doi.org/10.1139/cjm-2024-0248","url":null,"abstract":"<p><p>Fungal pathogens significantly impact human health, agriculture, and ecosystems, with infections leading to high morbidity and mortality, especially among immunocompromised individuals. The increasing prevalence of antifungal resistance (AFR) exacerbates these challenges, limiting the effectiveness of current treatments. Identifying robust biomarkers associated AFR could accelerate targeted diagnosis, shorten decision time for treatment strategies, and improve patient health. This paper examines traditional avenues of AFR biomarker detection, contrasting them with the increasingly effective role of machine learning (ML) in advancing diagnostic and therapeutic strategies. The integration of ML with technologies such as mass spectrometry, molecular dynamics, and various omics-based approaches often results in the discovery of diverse and novel resistance biomarkers. ML's capability to analyse complex data patterns enhances the identification of resistance biomarkers and potential drug targets, offering innovative solutions to AFR management. This paper highlights the importance of interdisciplinary approaches and continued innovation in leveraging ML to combat AFR, aiming for more effective and targeted treatments for fungal infections.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":"71 ","pages":"1-13"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954560","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":"Food-borne microbes influence conjugative transfer of antimicrobial resistance plasmids in pre-disturbed gut microbiome.","authors":"Marie Ottenbrite, Gokhan Yilmaz, Maria Chan, John Devenish, Mingsong Kang, Hanhong Dan, Calvin Ho-Fung Lau, Sabrina Capitani, Catherine Carrillo, Kyrylo Bessonov, John H E Nash, Edward Topp, Jiewen Guan","doi":"10.1139/cjm-2024-0168","DOIUrl":"10.1139/cjm-2024-0168","url":null,"abstract":"<p><p>Ingestion of antibiotic-resistant bacteria following antibiotic treatments may lead to the transfer of antimicrobial resistance genes (ARGs) within a disturbed gut microbiota. However, it remains unclear whether and how microbes present in food matrices influence ARG transfer. Thus, a previously established mouse model, which demonstrated the conjugative transfer of a multi-drug resistance plasmid (pIncA/C) from <i>Salmonella</i> Heidelberg (donor) to <i>Salmonella</i> Typhimurium (recipient), was used to assess the effects of food-borne microbes derived from fresh carrots on pIncA/C transfer. Mice were pre-treated with ampicillin, streptomycin, sulfamethazine, or left untreated as a control to facilitate bacterial colonization. Contrary to previous findings where high-density colonization of the donor and recipient bacteria occurred in the absence of food-borne microbes, the presence of these microbes resulted in a low abundance of <i>S</i>. Typhimurium and no detection of <i>S</i>. Typhimurium transconjugants in the fecal samples from any of the mice. However, in mice pre-treated with streptomycin, a significant reduction in microbial species richness allowed for the significant enrichment of <i>Enterobacteriaceae</i> and pIncA/C transfer to bacteria from the genera <i>Escherichia, Enterobacter, Citrobacter</i>, and <i>Proteus</i>. These findings suggest that food-borne microbes may enhance ARG dissemination by influencing the population dynamics of bacterial hosts within a pre-disturbed gut microbiome.</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":"143974154","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":"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":"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":"Effect of cannabidiol (CBD), a cannabis plant derivative, against <i>Candida albicans</i> growth and biofilm formation.","authors":"Maryam Bahraminia, Shujun Cui, Ze Zhang, Abdelhabib Semlali, Étienne Le Roux, Kelly-Anne Giroux, Camille Lajoie, François Béland, Mahmoud Rouabhia","doi":"10.1139/cjm-2024-0034","DOIUrl":"10.1139/cjm-2024-0034","url":null,"abstract":"<p><strong>Highlights: </strong>Cannabidiol (CBD) decreases the growth of <i>C. albicans</i>. CBD inhibits the yeast-to-hyphae transition. CBD reduces biofilm formation by <i>C. albicans</i>. CBD induces <i>C. albicans</i> death through necrosis.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-13"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142458629","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}