Cristina Spadari, Fernanda Ribeiro Dos Santos Esposito, Elder Sano, Caroline Cotrim Aires, Juliana Amorim Conselheiro, Gisely Toledo Barone, Adriana Araújo Reis-Menezes, Danielle Bruna Leal de Oliveira, Edison E L D Luiz Durigon, Jorge Sampaio, Nilton Lincopan, Kelly Ishida
{"title":"High prevalence of Candida species in the respiratory tract of patients diagnosed with SARS-CoV-2.","authors":"Cristina Spadari, Fernanda Ribeiro Dos Santos Esposito, Elder Sano, Caroline Cotrim Aires, Juliana Amorim Conselheiro, Gisely Toledo Barone, Adriana Araújo Reis-Menezes, Danielle Bruna Leal de Oliveira, Edison E L D Luiz Durigon, Jorge Sampaio, Nilton Lincopan, Kelly Ishida","doi":"10.1139/cjm-2025-0153","DOIUrl":"https://doi.org/10.1139/cjm-2025-0153","url":null,"abstract":"<p><p>Coinfection and secondary infection by fungi in patients with viral pulmonary infection, especially SARS-CoV-2, are important factors that worsen the prognosis and are associated to increased death rates. This work aims to report the prevalence of Candida isolates in bronchoalveolar and nasopharyngeal samples from suspected COVID-19 patients in the first-second pandemic waves and their antifungal resistance profile. From 2,321 patients, 29.04 % were diagnosed with SARS-CoV-2 infection. The yeast isolation rate of 6.97 % (47/674) from positive SARS-CoV-2 was statistically higher than 4.43% (73/1647) from negative SARS-CoV-2 patients (p=0.0177). Among yeasts, the most prevalent species was Candida albicans (63/120), with four being azole-resistant isolates (6.35%); however other emerging and less susceptible species were also isolated, such as Candida guilliermondii (11), Candida glabrata (5), Candida lusitaniae (4), Candida krusei (1), and Candida norvegensis (1). Here, we highlighted Candida prevalence in respiratory tract, emphasizing the relevance for surveillance in SARS-CoV-2/COVID patients for improvement of management as well as patient outcomes.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243770","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":"Osmotic stress tolerance and virulence of Salmonella enterica Tennessee and Serogroup B strains from low-moisture foods.","authors":"Adrián Gómez-Baltazar, Angélica Godínez-Oviedo, Ma Soledad Vázquez-Garcidueñas, Gerardo Vázquez-Marrufo, Montserrat Hernández-Iturriaga","doi":"10.1139/cjm-2025-0067","DOIUrl":"https://doi.org/10.1139/cjm-2025-0067","url":null,"abstract":"<p><p>Salmonella enterica is a major foodborne pathogen capable of surviving in low-water-activity (aW) foods and retaining the ability to invade intestinal epithelial cells after environmental stress, such as exposure to high salt concentrations. Although multiple serotypes tolerate low aW, Tennessee strains have been repeatedly linked to outbreaks in dry foods, suggesting specific adaptations. This study evaluated the effects of NaCl (1%, 4%, and 6%) on growth, biofilm formation, post-biofilm recovery, and internalization capacity (Caco-2 cell assays) of six S. enterica strains-four Tennessee and two serogroup B isolates-from peanuts, raisins, chocolate, and dehydrated tomatoes. Growth and biofilm formation were monitored over a 7-day exposure to NaCl; post-biofilm recovery and internalization were assessed afterward. While all strains showed reduced internalization after salt exposure, Tennessee isolates generally maintained higher growth and biofilm formation than the ATCC 14028 reference strain. Phenotypic responses varied by strain and NaCl concentration, indicating differences in osmotic stress adaptation. The persistence of internalization capacity, even at reduced levels, highlights a potential food safety risk in NaCl-preserved products. These findings emphasize the need to consider strain-specific traits when developing control measures for Salmonella in dry food environments.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211791","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":"Simplified and Efficient Agrobacterium-Mediated Genetic Transformation of Botrytis cinerea Using Mycelia.","authors":"Fayruza Lalany, Peter Moffett","doi":"10.1139/cjm-2025-0085","DOIUrl":"https://doi.org/10.1139/cjm-2025-0085","url":null,"abstract":"<p><p>Botrytis cinerea is a necrotrophic fungal pathogen responsible for grey mold disease, causing significant crop losses globally. Effective genetic manipulation of this pathogen is crucial for understanding its biology and developing better disease management strategies. However, current transformation methods typically use conidia spores or protoplasts, processes that are labor-intensive, inefficient, and often yield inconsistent results. We developed a novel Agrobacterium-mediated transformation protocol that utilizes B. cinerea mycelia, eliminating the need for sporulation or protoplast generation and simplifying genetic manipulation. Using a newly constructed binary expression vector encoding green fluorescent protein and hygromycin resistance, we transformed four different B. cinerea strains. All transformations resulted in stable integration and robust green fluorescent protein expression, confirmed by quantitative polymerase chain reaction and confocal microscopy. Although transformants exhibited altered colony morphology compared to wild-type strains, they remained viable and stably expressed the integrated transgene, supporting the method's utility for genetic studies in B. cinerea. This streamlined method provides a reliable, efficient, and scalable approach for genetic studies in B. cinerea, significantly enhancing fungal functional genomics research and plant pathology investigations.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124358","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":"Regulation of Pyrimidine Ribonucleoside Salvage Metabolism in Pseudomonas putida ATCC 17536.","authors":"Sara Fatima, Thomas P West","doi":"10.1139/cjm-2025-0161","DOIUrl":"https://doi.org/10.1139/cjm-2025-0161","url":null,"abstract":"<p><p>Pyrimidine base and ribonucleoside salvage metabolism was investigated in Pseudomonas putida ATCC 17536 cells. In ATCC 17536 cell extracts, the pyrimidine ribonucleoside salvage enzymes nucleoside hydrolase and cytosine deaminase activities were measurable while uridine phosphorylase activity was not. Carbon and nitrogen sources influenced the levels of the salvage pathway enzyme activities in P. putida ATCC 17536. Catabolite repression by a glucose metabolite of nucleoside hydrolase and cytosine deaminase synthesis in ATCC 17536 cells compared to cells grown on the carbon source succinate or ribose was observed while a nitrogen metabolite appeared to be controlling pyrimidine salvage enzyme synthesis. When glucose was the carbon source, ATCC 17536 cells grown on uracil or 5-methylcytosine as a nitrogen source caused at least a 5-fold increase in hydrolase and deaminase synthesis relative to their activities in ammonium sulfate-grown cells. In succinate-grown ATCC 17536 cells, thymine or 5-methylcytosine as a nitrogen catabolite produced at least double the hydrolase or deaminase activity relative to either activity in ammonium sulfate-grown cells. Overall, the pyrimidine base and ribonucleoside salvage enzymes in P. putida ATCC 17536 biovar B cells were regulated by the carbon or nitrogen source with pyrimidine salvage metabolism differing in biovar A and B strains.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124271","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}
Daniela Jaikel-Víquez, Fridha García-Sánchez, Isaac Santamaría-Sánchez, Stefany Lozada-Alvarado, Alejandra Gómez-Arrieta, Fabio Granados-Chinchilla, Laura Monturiol-Gross, Norma T Gross, Mauricio Redondo-Solano
{"title":"Isolation and characterization of potentially ochratoxigenic fungi from Costa Rican coffee (Coffea arabica L.) beans.","authors":"Daniela Jaikel-Víquez, Fridha García-Sánchez, Isaac Santamaría-Sánchez, Stefany Lozada-Alvarado, Alejandra Gómez-Arrieta, Fabio Granados-Chinchilla, Laura Monturiol-Gross, Norma T Gross, Mauricio Redondo-Solano","doi":"10.1139/cjm-2025-0088","DOIUrl":"https://doi.org/10.1139/cjm-2025-0088","url":null,"abstract":"<p><p>Coffee plants and beans are prone to fungal contamination that pose health risks to consumers by producing mycotoxins like ochratoxin A (OTA). Thus, the present study aimed to analyze the mycobiota of Costa Rican coffee beans, focusing on potentially ochratoxigenic species and their in vitro susceptibility patterns to antifungal agents. Fungal isolates were obtained from cherry, green, and roasted coffee beans from Costa Rica; they were identified by morphology, MALDI-TOF technology, and sequencing. The isolation frequency (FR) was 33.10 % for all the samples analyzed, 49.51 % for the cherry fruits, 37.67 % for the green coffee beans, and 17.33 % for the roasted beans. The cherry beans were mainly contaminated with Geotrichum klebahni (46.34 % FR and 90.91 % relative density [RD]), while the green and roasted coffee beans were mainly infected with Aspergillus spp. (22.00 % FR and 55.23 % RD and 13.83 % FR and 77.57 % RD, respectively). A total of 46.67 % of A. westerdijkiae and 20.00 % of A. ochraceus produced fluorescence in YES broth related with ochratoxin production. The isolates of the Aspergillus section Circumdati were susceptible to the azole antifungals. Costa Rican coffee beans could be contaminated with mycotoxigenic fungi during storage.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028943","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}
Bright Boamah, Ruimin Gao, Samuel Chekabab, Sohail Naushad, Xianhua Yin, Moussa Diarra, Dele Ogunremi
{"title":"Transcriptomic Analysis of Iron Transport mutants Reveals Serovar-Specific Adaptations in Salmonella enterica.","authors":"Bright Boamah, Ruimin Gao, Samuel Chekabab, Sohail Naushad, Xianhua Yin, Moussa Diarra, Dele Ogunremi","doi":"10.1139/cjm-2025-0011","DOIUrl":"https://doi.org/10.1139/cjm-2025-0011","url":null,"abstract":"<p><p>Iron is an essential mineral for almost all pathogenic bacteria including Salmonella enterica serovar Typhimurium and Enteritidis. We have investigated the effect of the deletion of iroN, fepA and fhu genes on the transcriptomic profiles of S. Typhimurium and S. Enteritidis strains containing double (ΔiroNΔfepA) and triple (ΔfhuΔiroNΔfepA) deletions and grown under iron-deficient conditions. Significant changes were observed in the expression of genes involved in virulence, stress-response, and energy metabolism in both Salmonella serovars. The pathways most affected were the tricarboxylic acid cycle, electron transport chain, and stress responses all of which were downregulated while cysteine biosynthesis was upregulated. In general, common and/or related genes were affected in the double and triple mutant strains which indicated that the additional deletion of the fhu gene affected a limited number of genes, although S. Typhimurium showed more differences than S. Enteritidis. Nevertheless, the main difference observed between the mutants of the two serovars grown under iron-depleted conditions is the enhanced upregulation of the flagellum genes in S. Enteritidis. This study reveals evidence of novel interactions between metabolic pathways and virulence under iron limitation, providing insights into adaptive strategies that may contribute to the enhanced virulence of these Salmonella serovars.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144944180","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}
Maysa Niazy, Heather M Murphy, Khurram Nadeem, Nicole Ricker
{"title":"A Comprehensive Guide to Selecting the Right Modeling Strategy for Explanatory and Predictive Data Analysis.","authors":"Maysa Niazy, Heather M Murphy, Khurram Nadeem, Nicole Ricker","doi":"10.1139/cjm-2025-0038","DOIUrl":"10.1139/cjm-2025-0038","url":null,"abstract":"<p><p>Declining costs of sequencing technology have catalyzed the widespread use of high-dimensional complex omics datasets in microbiology. While rich in information, these datasets present major analytical challenges, including sparsity, heterogeneity, and the need for robust statistical validation. Concerns about the reproducibility of findings across microbiological studies underscore the importance of standardized, transparent analytical approaches. Despite the availability of diverse statistical frameworks and machine learning methods, designing an appropriate statistical workflow (from method selection to model evaluation) remains challenging, particularly for researchers with limited advanced statistical training. Missteps in this process can lead to misinterpretation, irreproducibility, and flawed conclusions. This paper provides a structured, step-by-step framework to guide and validate the methodology of choosing the right statistical methods for both explanatory and predictive modeling in microbiology and translational research. We outline essential decision points spanning data preprocessing, feature selection, model assumptions, and model evaluation, and highlight common trade-offs and practical considerations. To demonstrate the guide's utility, we analyze a real-world COVID-19 dataset to identify cytokine biomarkers associated with disease severity. By aligning analytical strategies with microbiology inquiry, this guide aims to enhance reproducibility, empower data-informed decisions, and promote more rigorous, interpretable research in microbiology and public health.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871605","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}