Canadian journal of microbiology最新文献

{"title":"Engineering Conjugative Plasmids for Inducible Horizontal DNA Transfer.","authors":"Tahani Jaafar, Emily Carvalhais, Arina Shrestha, Ryan R Cochrane, Jordyn S Meaney, Stephanie Brumwell, Samir Hamadache, Vida Nasrollahi, Bogumil Karas","doi":"10.1139/cjm-2024-0241","DOIUrl":"https://doi.org/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 cis and trans 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":""},"PeriodicalIF":1.8,"publicationDate":"2025-04-01","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":"An epidemiological framework for improving the accuracy of whole-genome sequence-based antimicrobial resistance surveillance in Salmonella.","authors":"Benjamin Hetman, David L Pearl, Richard Reid-Smith, Jane Parmley, Eduardo Taboada","doi":"10.1139/cjm-2024-0090","DOIUrl":"https://doi.org/10.1139/cjm-2024-0090","url":null,"abstract":"<p><p>Whole-genome sequence-based surveillance of bacteria for determinants of antimicrobial resistance promises many advantages over traditional, wet-lab approaches. However, adjustments to parameters used to identify genetic determinants from sequencing data can affect results and interpretation of the important determinants in circulation. Using a dataset of whole-genome sequences from 1633 isolates of Salmonella Heidelberg and S. Kentucky collected from surveillance of Canadian poultry production, we queried the genomic data using an in-silico AMR detection tool, StarAMR, applying a range of parameter values required for the detection pipeline to test for differences in detection accuracy. We compared the results from each iteration to phenotypic antimicrobial susceptibility results, and generated estimates of sensitivity and specificity using regression models that controlled for the effects of multiple sampling events and variables, and interactions between covariates. Results from our analyses revealed small, yet significant effects of the input parameters on the sensitivity and specificity of the AMR detection tool, and these effects differed based on the serovar and drug class in question. Findings from this study may have implications for the incorporation of whole-genome sequence-based approaches to the surveillance of antimicrobial resistance determinants in bacteria sampled from food products and animals related to food production.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656232","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":"Interactions between common scab-inducing strains on potato suberin.","authors":"Mario Khalil Habeeb Khalil, Iauhenia Isayenka, Rebeca Padilla-Reynaud, Sylvain Lerat, Carole Beaulieu","doi":"10.1139/cjm-2024-0242","DOIUrl":"https://doi.org/10.1139/cjm-2024-0242","url":null,"abstract":"<p><p>Potato tuber periderm is armored with suberin, that consists of two domains, an aliphatic domain composed of fatty acid polyesters and an aromatic domain composed of cinnamic acids. Streptomyces scabies 87.22, a predominant causal agent of potato common scab, was compared for adaptation to tuber suberin with Streptomyces acidiscabies ATCC 49003 and Streptomyces turgidiscabies Car8 belonging to emerging pathogenic species. S. scabies 87.22 showed higher growth in the suberin supplemented medium than the two other strains. When co-cultured on rich nutrient medium, S. acidiscabies ATCC 49003 produced the antibiotic oxanthromicin, which inhibited growth and mycelium development of the other strains. Exposure of S. scabies 87.22 and S. acidiscabies ATCC 49003 to suberin was accompanied by the secretion of enzymes degrading cellulose, hemicellulose, fatty acids and glycerol derivatives. Compared to the two other strains, S. scabies 87.22 showed higher esterase activity in suberin-supplemented medium and strong induction of cellulase gene expression. Both S. acidiscabies ATCC 49003 and S. turgidiscabies Car8 exhibited a poor utilization of trans-ferulic and p-coumaric acids, suggesting almost no ability to degrade the aromatic moiety of suberin. This work suggests that S. scabies 87.22 is better adapted to the potato periderm degradation than the emerging pathogens. The elucidation of pathogenic Streptomyces strains interaction may contribute to the improvement of ecologically oriented agronomic strategies for common scab management.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630201","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":"Molecular epidemiology and in silico prediction of ciprofloxacin resistance in Salmonella enterica in Canada, 2017-2022.","authors":"MacKenzie A P Wilke, Ketna Mistry, David Thumbi, Xiao Rui Lisa Li, Audrey Charlebois, Ashley C Cormier, Katrina Mickanuck, Brent P Avery, Colleen Murphy, Anne Deckert, Ashley Kearney, Jennifer Campbell, Sara Christianson, David Alexander, Sameh El Bailey, Sadjia Bekal, Linda Chui, Xiaofeng Ding, Tanis C Dingle, David Haldane, Linda Hoang, Jessica Minion, Samir Patel, George Zahariadis, Celine Nadon, Michael Mulvey, Carolee A Carson, Richard Reid-Smith, Amrita Bharat","doi":"10.1139/cjm-2024-0118","DOIUrl":"https://doi.org/10.1139/cjm-2024-0118","url":null,"abstract":"<p><p>Ciprofloxacin is important for treatment of severe or invasive Salmonella infections in humans. As laboratories transition from phenotypic to genomics-based methods for determining ciprofloxacin non-susceptibility, it is important to define the correlation between genetic determinants of resistance and phenotypic outcomes. Here, we examined ciprofloxacin resistance mechanisms in Salmonella and tested the hypothesis that isolates containing only one mechanism had intermediate resistance while isolates containing two or more mechanisms had full resistance according to breakpoints from the Clinical Laboratory Standards Institute. Among 13,750 human and food/animal Salmonella enterica isolates, 2325 were predicted to be non-susceptible to ciprofloxacin using whole genome sequencing and Staramr. The most common mechanisms of resistance were mutations in gyrA (especially S83F and D87N/D87Y) and the qnrB19 allele. Only 28% of ciprofloxacin resistant isolates had two or more resistance mechanisms; the remainder contained only one mechanism. Of isolates with two or more mechanisms, only 63% were resistant. Thus, the number of genetic determinants of ciprofloxacin resistance in an isolate could not reliably differentiate the ciprofloxacin intermediate or resistant categories when using North American breakpoints. Predicting ciprofloxacin intermediate/resistant as a single non-susceptible category would facilitate global standardization of data to inform public health surveillance, treatment guidelines and stewardship.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603932","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":"Correction: Characterization and whole-genome sequencing of an extreme arsenic tolerant <i>Citrobacter freundii</i> SRS1 strain isolated from Savar area in Bangladesh.","authors":"Mohammed Jafar Uddin, Farhana Haque, Ishrat Jabeen, Sabbir R Shuvo","doi":"10.1139/cjm-2024-0195","DOIUrl":"10.1139/cjm-2024-0195","url":null,"abstract":"","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833903","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":"Development and evaluation of a sensitive approach for detection and recovery of third-generation cephalosporin- and carbapenem-resistant Enterobacterales from ready-to-eat frozen stone fruit.","authors":"Adeeb Nasta, Ashley L Cooper, Irelynd V Tackabury, Chloe Anastasiadis, Calvin Ho-Fung Lau, Liam P Brown, Myron L Smith, Sandeep Tamber, Catherine D Carrillo","doi":"10.1139/cjm-2024-0210","DOIUrl":"10.1139/cjm-2024-0210","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) is a global public health threat, but the role of foods in its dissemination is poorly understood. We examined the incidence of foodborne bacteria carrying AMR genes considered high-priority research targets by the World Health Organization. Frozen, ready-to-eat, avocado, coconut, mango, and peach (<i>n</i> = 161) were tested for bacteria encoding extended-spectrum β-lactamases (ESBLs) and carbapenemases. Over 600 presumptive-positive isolates were recovered and analyzed with a pooled sequencing (Pool-seq) strategy. Coconut samples exhibited the highest bacterial loads and prevalence/diversity of AMR genes. Isolates harbouring the β-lactamase genes <i>bla</i>_ctx-m, <i>bla</i>_tem, and <i>bla</i>_shv, identified in 14 coconut and 2 mango samples, were further characterized by whole-genome sequencing and antimicrobial susceptibility testing. The most common gene was <i>bla</i>_ctx-m-15, detected in 20 unique strains. Two carbapenemase-producing strains were isolated from coconut: <i>Enterobacter roggenkampii</i> encoding <i>bla</i>_ndm-1 and <i>Escherichia coli</i> encoding <i>bla</i>_ndm-5. Subsequent quantitative PCR (qPCR) analysis of enrichments for <i>bla</i>_ctx-m/<i>bla</i>_ndm indicated a potentially higher prevalence of these genes than observed by colony screening. This study presents a practical method for recovering ESBL- and carbapenemase-producing bacteria from foods. Mapping their distribution in food products is crucial to assessing the role of foods in the global spread of AMR and developing effective public health interventions.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-18"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143498289","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":"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":"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}