Mohannad Mahmoud, Philippe Seguin, Sébastien P Faucher, Suha Jabaji
{"title":"Characterization and antifungal properties against <i>Botrytis cinerea</i> of bacteria isolated from hemp seed oil.","authors":"Mohannad Mahmoud, Philippe Seguin, Sébastien P Faucher, Suha Jabaji","doi":"10.1139/cjm-2025-0241","DOIUrl":"10.1139/cjm-2025-0241","url":null,"abstract":"<p><p><i>Botrytis cinerea</i> is a pathogen infecting <i>Cannabis sativa</i> L. plants, causing economic losses, and can develop resistance to chemical fungicides, the use of which is restricted in cannabis production. Thus, developing biocontrol methods is imperative. Seven bacterial strains were isolated from hemp seed oil, characterized, and examined for the potential to control a <i>Botrytis cinerea</i> isolate from cannabis. Three isolates, <i>Bacillus mojavensis</i> HOB3, <i>Paenibacillus</i> sp. HOB6, and <i>Bacillus subtilis</i> HOB7 exhibited significant inhibition of <i>Botrytis cinerea.</i> These isolates were further evaluated for their biosurfactant activity using two liquid media, Lysogeny Broth (LB) and hydrocarbon-amended Bushnell and Haas (BH). The oil-spreading and drop-collapse assays revealed growth-medium-dependent variation in surface activity associated with biosurfactant presence. The BH cell-free extract (BH-CFE) of <i>Bacillus subtilis</i> HOB7 showed the highest estimated biosurfactant presence and antifungal activity against <i>Botrytis cinerea</i>, but both activities were absent when using the LB cell-free extract (LB-CFE) of <i>Bacillus subtilis</i> HOB7. Thus, a potential relationship between antifungal activity and biosurfactant production was suggested. Genome mining of the strains identified gene clusters encoding compounds with antifungal activity, including the biosurfactants polymyxin B, fusaricidin B, fengycin, and surfactin. To our knowledge, this is the first report of the isolation of hemp seed oil bacteria with potential biocontrol properties against fungal phytopathogens.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-15"},"PeriodicalIF":1.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145687042","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":"Epidemiology and impact of high pathogenicity avian influenza in Europe 2020-2025.","authors":"Ian H Brown, Chris Neil","doi":"10.1139/cjm-2025-0214","DOIUrl":"10.1139/cjm-2025-0214","url":null,"abstract":"<p><p>High pathogenicity avian influenza (HPAI) of H5 subtype was detected year-round for the first time in Europe in 2022 and contributed to the largest European HPAI epizootic. The switch from H5N8 to H5N1 virus subtypes heralded a substantial increase in cases in wild and domestic birds. The impact on domestic poultry production was substantial with more than 120 million birds dying or being culled to control the disease. This was partly attributed to an expansion in the host range of wild birds affected, with infection of orders of birds not previously described as susceptible. The consequence of these transmission events into naive wild bird populations was often large-scale mortality, particularly in seabirds 2022-2023. Relatively high infection pressure provided opportunity for exposure and spillover to wild mammals principally of the order Carnivora, exposed through predatory or scavenging behaviour. Other sporadic infections involved farmed fur animals and a single detection in a sheep in England, but no evidence of infection in other livestock species including dairy cattle. Human infections were rare and asymptomatic, associated with very close contact with infected domestic birds. The epizootic was sustained by continuing evolution in the virus principally through genetic reassortment with selection and fixation of genotypes of high fitness in the avian population.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-11"},"PeriodicalIF":2.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146017422","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":"Parallel evolutionary trajectories of extensively drug-resistant <i>Klebsiella pneumoniae</i> ST258 and ST307 pandemic clones: a systematic review.","authors":"Sampurna Nivedita Sarkar, Surojit Das","doi":"10.1139/cjm-2025-0268","DOIUrl":"10.1139/cjm-2025-0268","url":null,"abstract":"<p><p>Extensively drug-resistant (XDR) <i>Klebsiella pneumoniae</i> poses a critical threat to global public health. ST258 and ST307 are two pandemic clones that have emerged through distinct evolutionary mechanisms. Understanding their parallel trajectories is essential for clinical management and therapeutic development. This systematic review examined peer-reviewed literature on <i>K. pneumoniae</i> ST258 and ST307 (1995-2025) from PubMed, Scopus, Google Scholar, and Web of Science. We extracted data on resistance genes, virulence factors, geographic distribution, and clinical outcomes. Inclusion criteria: studies with molecular or genomic characterization of ST258/ST307 isolates. Analysis revealed distinct evolutionary pathways. ST258 (emerged 1995, USA) showed recombination driven evolution with stable <i>bla</i><sub>KPC-2/3</sub> resistance, remaining hospital-endemic and declining after 2015. ST307 (emerged 2008, Netherlands) demonstrated plasmid-mediated adaptability with diverse carbapenemases (<i>bla</i><sub>NDM</sub>, <i>bla</i><sub>OXA-48</sub>, <i>bla</i><sub>KPC</sub>), achieving rapid global dissemination across six WHO regions by 2025. Both achieved pandemic status through different mechanisms. ST307 shows emerging hypervirulent sublineages in Europe and South America. Two distinct evolutionary strategies converge to create a unified pandemic threat. ST258's stability contrasts with ST307's adaptability, reflecting different fitness landscapes. Both clones exhibit limited susceptibility to current therapeutic options, with emerging resistance to last-resort agents. ST258 and ST307 represent complementary pandemic threats requiring coordinated global surveillance, antimicrobial development, and research into evolutionary dynamics.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-12"},"PeriodicalIF":2.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147472399","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}
Jaime Daniel Babot, Víctor Maximiliano Hidalgo, María Magdalena Fernández, Horacio Raúl Terzolo, Adriana Perez Chaia, María Cristina Apella
{"title":"Preventive effects of synbiotic supplementation against <i>Salmonella</i> Enteritidis infection in broiler chickens.","authors":"Jaime Daniel Babot, Víctor Maximiliano Hidalgo, María Magdalena Fernández, Horacio Raúl Terzolo, Adriana Perez Chaia, María Cristina Apella","doi":"10.1139/cjm-2025-0283","DOIUrl":"10.1139/cjm-2025-0283","url":null,"abstract":"<p><p>The restriction of antibiotics as growth promoters in poultry has intensified the search for alternative strategies to control enteric pathogens. This study aimed to develop a multi-strain probiotic composed of <i>Enterococcus faecium</i> CRL 1385, <i>Ligilactobacillus salivarius</i> subsp. <i>salivarius</i> CRL 1417, and <i>Lactobacillus crispatus</i> CRL 1453, formulate a synbiotic by combining this mixture with raffinose and molasses, and evaluate their preventive efficacy against <i>Salmonella</i> infection in broiler chicks. Strain compatibility was assessed using a well-diffusion assay with cell-free supernatants, confirming absence of antagonism among strains. <i>In vitro</i> co-culture assays demonstrated a clear bactericidal effect, with inactivation of <i>Salmonella</i> Enteritidis PT4 1222 and <i>Salmonella</i> Gallinarum INTA 91/A1. <i>Ex vivo</i> assays using intestinal explants showed that pre-treatment with probiotic or synbiotic formulations significantly reduced <i>Salmonella</i> adhesion, suggesting that the primary protective mechanism involved inhibition of pathogen attachment to epithelial surfaces. For <i>in vivo</i> evaluation, chicks received daily treatments from day 1 post-hatch and were challenged via crop injection on day 3. Synbiotic administration significantly reduced <i>S.</i> Enteritidis infection rates (30% vs. 100% in controls), while all treatments failed to reduce <i>S.</i> Gallinarum prevalence. These findings highlight the potential of early-life synbiotic administration as a sustainable strategy to prevent <i>S.</i> Enteritidis infections in poultry.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-12"},"PeriodicalIF":2.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147484689","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}
Manuel Jara, Alba Frias-De-Diego, Robert A Petit, Loc Nguyen, Cristina Lanzas
{"title":"Pangenome-GWAS analysis of <i>Clostridioides difficile</i> resistant traits from healthcare- and non-healthcare-associated settings.","authors":"Manuel Jara, Alba Frias-De-Diego, Robert A Petit, Loc Nguyen, Cristina Lanzas","doi":"10.1139/cjm-2025-0288","DOIUrl":"10.1139/cjm-2025-0288","url":null,"abstract":"<p><p><i>Clostridioides difficile</i> (<i>C. difficile</i>) is a gastrointestinal pathogen that causes healthcare-associated infections with numerous mechanisms to acquire and confer antimicrobial resistance (AMR) and rapidly adapt to novel environments. These environments extend beyond healthcare, and encompass non-healthcare-related settings, where antimicrobials engender distinct selection pressures. Employing a dataset of 3870 whole-genome sequences of <i>C. difficile</i> from healthcare and non-healthcare environments, this study investigates the selection pressures associated with each setting and its impact on the prevalence of AMR genes of <i>C. difficile.</i> To achieve this, we used pangenome-wide association studies (pan-GWAS) and generalized linear mixed model to identify significant associations between AMR genes and the specific setting from which the isolates were collected. Our findings evidenced significant differences in the AMR gene repertoire between healthcare- and non-healthcare-associated <i>C. difficile</i> with antibiotics such as macrolides and fluoroquinolones being more linked with healthcare. Antibiotics commonly used in agriculture such as aminoglycosides or tetracyclines also presented associations with non-healthcare environments. Our work offers a comprehensive exploration of <i>C. difficile</i> AMR determinants across healthcare- and non-healthcare-related settings shedding light on the selection pressures present in each environment, enhancing our understanding of <i>C. difficile</i> resistome and its influence on the bacterium's opportunistic colonization nature.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-11"},"PeriodicalIF":2.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13177613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147509822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Éléonore Lemieux, Laurie C Piché, Sabrina A Attéré, Mikaël Charette, Viacheslav Liato, Rodrigue Dubar, Simon J Labrie, Linda Saucier, Antony T Vincent
{"title":"From one host to another: adaptation of a phage infecting avian pathogenic <i>Escherichia coli</i> to the laboratory strain K-12.","authors":"Éléonore Lemieux, Laurie C Piché, Sabrina A Attéré, Mikaël Charette, Viacheslav Liato, Rodrigue Dubar, Simon J Labrie, Linda Saucier, Antony T Vincent","doi":"10.1139/cjm-2026-0049","DOIUrl":"10.1139/cjm-2026-0049","url":null,"abstract":"<p><p>Avian colibacillosis is an infectious disease that causes significant economic losses worldwide in the poultry industry. The bacterium avian pathogenic <i>Escherichia coli</i> (APEC) is the etiological agent of the disease and is primarily treated with antibiotics. Unfortunately, due to antibiotic resistance in APEC, therapeutic options for treating this disease are becoming increasingly limited. Bacteriophages-viruses that infect bacteria-represent promising therapeutic candidates; however, understanding how these viruses adapt is essential before considering them for commercial applications. This study investigated the adaptation of an APEC-infecting phage to a laboratory strain <i>E. coli</i> K-12 host. Successive passages of the phage on the K-12 strain resulted in clear adaptation to this new host, with only a slight fitness cost on APEC. The adapted phages also exhibited smaller capsids. Genomic comparison between the adapted phages and the wild-type phage revealed three mutations that may explain the adaptation to the K-12 strain: two point mutations located in a gene encoding a hypothetical protein and a 42-bp in-frame deletion in a homologue of the gene encoding the tail spike protein TSP4. This study, in addition to identifying molecular determinants involved in the adaptation of an APEC-infecting phage, further highlights the remarkable capacity of viruses to evolve.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-9"},"PeriodicalIF":2.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148469118","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}
Mario Khalil, Iauhenia Isayenka, Rebeca Padilla-Reynaud, Sylvain Lerat, Carole Beaulieu
{"title":"Interactions between common scab-inducing strains on potato suberin.","authors":"Mario Khalil, Iauhenia Isayenka, Rebeca Padilla-Reynaud, Sylvain Lerat, Carole Beaulieu","doi":"10.1139/cjm-2024-0242","DOIUrl":"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. <i>Streptomyces scabies</i> 87.22, a predominant causal agent of potato common scab, was compared for adaptation to tuber suberin with <i>Streptomyces acidiscabies</i> ATCC 49003 and <i>Streptomyces turgidiscabies</i> Car8 belonging to emerging pathogenic species. <i>Streptomyces scabies</i> 87.22 showed higher growth in the suberin supplemented medium than the two other strains. When co-cultured in a rich nutrient medium, <i>S. acidiscabies</i> ATCC 49003 produced the antibiotic oxanthromicin, which inhibited growth and mycelium development of the other strains. Exposure of <i>S. scabies</i> 87.22 and <i>S. acidiscabies</i> 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, <i>S. scabies</i> 87.22 showed higher esterase activity in suberin-supplemented medium and strong induction of cellulase gene expression. Both <i>S. acidiscabies</i> ATCC 49003 and <i>S. turgidiscabies</i> Car8 exhibited a poor utilization of <i>trans</i>-ferulic and <i>p</i>-coumaric acids, suggesting almost no ability to degrade the aromatic moiety of suberin. This work suggests that <i>S. scabies</i> 87.22 is better adapted to the potato periderm degradation than the emerging pathogens. The elucidation of pathogenic <i>Streptomyces</i> 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":"1-15"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","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}
Mohammed Jafar Uddin, Farhana Haque, Ishrat Jabeen, Sabbir R Shuvo
{"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":"<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":"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}
Janice Moat, Athanasios Zovoilis, Rylan Steinkey, Rahat Zaheer, Tim McAllister, Chad Laing
{"title":"Machine learning methods to identify markers and predict antimicrobial resistance in <i>Escherichia coli</i>.","authors":"Janice Moat, Athanasios Zovoilis, Rylan Steinkey, Rahat Zaheer, Tim McAllister, Chad Laing","doi":"10.1139/cjm-2024-0208","DOIUrl":"10.1139/cjm-2024-0208","url":null,"abstract":"<p><p>Antimicrobial resistant strains of pathogenic <i>Escherichia coli</i> are a burden on the healthcare system, causing longer hospital stays and increased treatment costs compared to nonresistant strains. With whole genome sequencing almost ubiquitous in the analyses of outbreak and surveillance samples<i>,</i> in silico methods for feature identification can be faster and cheaper than traditional wet-lab methods. In this study, machine learning (ML) classification methods were used to predict antimicrobial resistance (AMR) and identify novel genomic markers of resistance. A total of 4300 <i>E. coli</i> whole genome sequences with laboratory-derived susceptible, intermediate, or resistant (SIR) data for 34 antimicrobials were collected. Three models-gradient boosted decision trees, support vector machines (SVMs), and artificial neural networks (ANNs)-were trained using genome subsequences (<i>k</i>-mers) of length 11 to classify unknown isolates as SIR for each antimicrobial. The models achieved high average accuracies (93.6%, 92.7%, and 92.8%, respectively) for our dataset, outperforming database methods including AMRFinderPlus (63.9%) and ResFinder (75.7%). Tested on two smaller independent datasets, the models' average accuracies were 81.6% (XGB), 79.9% (SVM), and 81.2% (ANN), while ResFinder's average accuracy was 94.7%. An advantage of ML models over database methods is that they can identify novel markers of resistance, which is a key advantage for surveillance and research. As more genomic and AMR data become publicly available, these models are expected to further improve in performance and utility.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-15"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145387055","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}