Canadian journal of microbiology最新文献

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Microbial communities in the Hudson Strait amidst rapid environmental change. 快速环境变化中的哈德逊海峡微生物群落。
IF 1.8 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 DOI: 10.1139/cjm-2024-0154
Samantha J T Loutet, Alia Sanger, Kallie Strong, R Eric Collins, Nagissa Mahmoudi
{"title":"Microbial communities in the Hudson Strait amidst rapid environmental change.","authors":"Samantha J T Loutet, Alia Sanger, Kallie Strong, R Eric Collins, Nagissa Mahmoudi","doi":"10.1139/cjm-2024-0154","DOIUrl":"10.1139/cjm-2024-0154","url":null,"abstract":"<p><p>Climate change is rapidly altering Arctic marine environments, leading to warmer waters, increased river discharge, and accelerated sea ice melt. The Hudson Bay Marine System experiences the fastest rate of sea ice loss in the Canadian North resulting in a prolonged open water season during the summer months. We examined microbial communities in the Hudson Strait using high throughput 16s rRNA gene sequencing during the peak of summer, in which the bay was almost completely ice-free, and air temperatures were high. We found that salinity and temperature significantly affected the taxonomic composition among microbial communities across sites. We observed a higher relative abundance of specific <i>Polaribacter</i> sp. Amplicon sequence variants (ASVs) at more saline sites. Shannon diversity was not significantly impacted by salinity or temperature. These results contribute to our understanding of surface water microbial community composition in the Hudson Strait and shed light on how future salinity and temperature conditions may favour certain microbial populations.</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":"143027842","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}
引用次数: 0
A comprehensive guide to selecting the right modeling strategy for explanatory and predictive data analysis. 为解释和预测数据分析选择正确建模策略的综合指南。
IF 1.6 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 DOI: 10.1139/cjm-2025-0038
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":"1-18"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","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}
引用次数: 0
VeA is involved in anti-tumor activity by regulating adenylosuccinate lyase to mediate the synthesis of Acadesine in endophytic Fusarium solani. VeA通过调节内生镰刀菌中腺苷琥珀酸裂解酶介导乙酰胆碱的合成,参与抗肿瘤活性。
IF 1.8 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 DOI: 10.1139/cjm-2024-0073
Rongfei Liu, Wen Zheng, Lu Cai, Qing Xiao, Guihua Liu, Yuling Jiang, Zhangjiang He, Jichuan Kang
{"title":"VeA is involved in anti-tumor activity by regulating adenylosuccinate lyase to mediate the synthesis of Acadesine in endophytic <i>Fusarium solani</i>.","authors":"Rongfei Liu, Wen Zheng, Lu Cai, Qing Xiao, Guihua Liu, Yuling Jiang, Zhangjiang He, Jichuan Kang","doi":"10.1139/cjm-2024-0073","DOIUrl":"https://doi.org/10.1139/cjm-2024-0073","url":null,"abstract":"<p><p>Acadesine (AICAR) is a promising candidate for new drugs in Phase III clinical trials. The purpose of this study is to analyse the steps in the biosynthesis pathway of AICAR. Our previous study found that overexpression of <i>veA</i>, a gene encoding a global regulator, significantly increased AICAR production of endophytic <i>Fusarium solani</i> HB1-J1 and the anti-tumor activity of its extracts. Transcriptome and metabolome analysis of FsveA<sup>OE14</sup>, a <i>veA</i> overexpressing <i>F. solani</i> strain, revealed a 10-step AICAR synthesis pathway, with adenylosuccinate lyase PurB as a key enzyme. Generally, overexpressing <i>purB</i> (the gene encoding adenylosuccinate lyase) enhances AICAR synthesis. However, in FsveA<sup>OE14</sup>, despite down-regulation of <i>purB</i>, AICAR content increased, which is contradictory. Further studies revealed that expression levels of <i>purB</i> homologs gene, <i>pro06469</i> and <i>pro10879</i>, were upregulated in FsveA<sup>OE14</sup>. This suggests that although <i>veA</i> overexpression leads to <i>purB</i> down-regulation, their up-regulation may compensate for the reduction of <i>purB</i>, thus affecting AICAR synthesis. Additionally, compared to the wild type, overexpressing <i>purB</i> significantly enhances the inhibitory activity of the strain's extracts against the nonsmall-cell lung cancer cell line A549. Furthermore, it also increases the metabolic levels of other anti-tumor compounds, including 3-methyladenine, taurine, and others. These results indicate that VeA regulates AICAR biosynthesis via key enzymes like PurB, enhancing AICAR and other anti-tumor compound production, thus increasing the anti-tumor activity of <i>F. solani</i> extracts<i>.</i></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":"144552317","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}
引用次数: 0
Disruption of MAPK signalling and amino acid biosynthesis underlies the antifungal biocontrol mechanism of Coniochaeta velutina against Colletotrichum gloeosporioides: a transcriptome and metabolome analysis. MAPK信号传导和氨基酸生物合成的中断是绒毛Coniochaeta对炭疽菌的生物防治机制的基础:转录组和代谢组分析。
IF 1.6 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 DOI: 10.1139/cjm-2023-0223
Wei Zheng, Chunling Yang, Chengbo Zhou, Tianxiao Ma, Qingsong Zhu, Zhuoqi Li
{"title":"Disruption of MAPK signalling and amino acid biosynthesis underlies the antifungal biocontrol mechanism of <i>Coniochaeta velutina</i> against <i>Colletotrichum gloeosporioides</i>: a transcriptome and metabolome analysis.","authors":"Wei Zheng, Chunling Yang, Chengbo Zhou, Tianxiao Ma, Qingsong Zhu, Zhuoqi Li","doi":"10.1139/cjm-2023-0223","DOIUrl":"10.1139/cjm-2023-0223","url":null,"abstract":"<p><p><i>Colletotrichum gloeosporioides</i> is a destructive pathogen that causes significant economic and ecological losses in agricultural and forestry production. In search of effective biocontrol agents, this study isolated an endophytic fungus, <i>Coniochaeta velutina</i>, from healthy <i>Camellia oleifera</i> leaves and investigated its in vitro inhibitory mechanism on <i>Colletotrichum gloeosporioides</i> using transcriptomics and metabolomics analyses. These findings were used to evaluate the differences in gene expression and metabolite content between the treatment (<i>Coniochaeta velutina</i>-treated <i>Colletotrichum gloeosporioides</i>) and control (untreated <i>Colletotrichum gloeosporioides</i>) groups. The transcriptomic analysis detected a total of 15 310 expressed genes, with 3938 showing significant differential expression (<i>p</i> < 0.05) (2093 upregulated and 1845 downregulated genes). These genes were enriched primarily in the following pathways: mitogen-activated protein kinase (MAPK) signalling, antibiotic biosynthesis, amino acid metabolism, carbon metabolism, and peroxidase pathways. Metabolomic analysis revealed 452 metabolites in both groups, with 138 showing significant differences. These genes were enriched mainly in secondary metabolite biosynthesis, amino acid biosynthesis, and α-linolenic acid metabolism. Transcriptome and metabolome association analyses, along with qRT-PCR results, revealed that the levels of intracellular pectolinarigenin metabolites significantly increased in the treatment group, leading to disrupted MAPK signalling and reduced amino acid biosynthesis, which are essential for maintaining normal cell growth. Notably, the decrease in terpenoid compounds was the primary reason that <i>Colletotrichum gloeosporioides</i> was inhibited by the biocontrol fungus <i>Coniochaeta velutina.</i> Therefore, these findings provide valuable insights into the biocontrol mechanisms of <i>Coniochaeta velutina</i> against <i>Colletotrichum gloeosporioides</i> and offer a promising foundation for the development of new anthracnose prevention and control strategies.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-13"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118842","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}
引用次数: 0
Isolation, identification, and community study of root fungal isolates from disturbed and undisturbed Arctic and alpine tundra habitats in Northern Quebec, Canada. 加拿大魁北克北部受干扰和未受干扰北极和高山冻土带生境根真菌分离、鉴定和群落研究。
IF 1.6 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 DOI: 10.1139/cjm-2024-0211
Léonie Côté, Godar Sene, Marie-Eve Beaulieu, Stéphane Boudreau, Damase P Khasa
{"title":"Isolation, identification, and community study of root fungal isolates from disturbed and undisturbed Arctic and alpine tundra habitats in Northern Quebec, Canada.","authors":"Léonie Côté, Godar Sene, Marie-Eve Beaulieu, Stéphane Boudreau, Damase P Khasa","doi":"10.1139/cjm-2024-0211","DOIUrl":"10.1139/cjm-2024-0211","url":null,"abstract":"<p><p>In northern ecosystems such as the subarctic tundra, mining activities increase stress to a point where actions are needed to promote site reclamation. Ecological restoration of these mining-impacted sites with beneficial microorganisms, such as mycorrhizal fungi, is considered necessary and useful for the growth and survival of their host plants, but also for their tolerance to poor and contaminated environments, such as mine tailings. Here, we are interested in root symbionts associated with plants from the Schefferville mining site in northern Quebec. Very few studies of root fungal communities have been conducted in such a northern environment. The spatial and host plant variation of root fungal isolates was investigated. A total of 456 culturable fungi were isolated, of which 376 were successfully identified and assigned to 106 taxa based on rDNA internal transcribed spacer analysis using ITSF-1 and ITS-4 primers. The most commonly isolated fungi belonged to three genetically related groups: the <i>Rhizoscyphus ericae</i> aggregate, the dark septate endophytes, and <i>Umbelopsis rammaniana</i> and <i>Mortierella</i> sp., which are known to be genetically very close and often misclassified as one another. These groups were present on both disturbed and natural sites, but it appears that plants from disturbed sites had a greater affinity for dark septate endophytes. This study is the first step in the development of a restoration plan for the Schefferville mining site, and the baseline data obtained open new avenues for future studies, including the use of indigenous mycorrhizal-based biofertilizers to implement ecological revegetation strategies.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-13"},"PeriodicalIF":1.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144274246","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}
引用次数: 0
Carvacrol, a monoterpenoid, binds quorum sensing proteins (LasI and LasR) and swarming motility protein BswR of Pseudomonas aeruginosa, resulting in loss of pathogenicity: an in silico approach. 单萜类香芹酚能与铜绿假单胞菌的法定量感应蛋白(LasI 和 LasR)和蜂群运动蛋白 BswR 结合,从而导致铜绿假单胞菌失去致病性:硅学方法
IF 1.8 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 Epub Date: 2024-11-20 DOI: 10.1139/cjm-2024-0155
Susmita Datta, Vishal Singh, Soma Nag, Dijendra Nath Roy
{"title":"Carvacrol, a monoterpenoid, binds quorum sensing proteins (LasI and LasR) and swarming motility protein BswR of <i>Pseudomonas aeruginosa,</i> resulting in loss of pathogenicity: an in silico approach.","authors":"Susmita Datta, Vishal Singh, Soma Nag, Dijendra Nath Roy","doi":"10.1139/cjm-2024-0155","DOIUrl":"10.1139/cjm-2024-0155","url":null,"abstract":"<p><p>The pathogenic <i>Pseudomonas aeruginosa</i> utilizes a quorum-sensing pathway for biofilm formation. The quorum-sensing proteins LasI and LasR of the Las system, alongside the swarming motility protein BswR, play a crucial role in the biofilm-mediated antibiotic resistance phenomenon. In this in silico study, LasI, LasR, and BswR were the prime targets for binding studies by promising drug candidates like linalool, ferutinin, citronellal, and carvacrol. These monoterpenoid compounds are carefully considered for this study due to their reported anti-microbial activity. Among all, carvacrol exhibited the highest binding energies with LasI (-5.932 kcal/mol), LasR (-7.469 kcal/mol), and BswR (-4.42 kcal/mol). Furthermore, the MMGBSA scores between carvacrol and LasI, LasR, and BswR individually are -33.14, -54.22, and -41.86 kcal/mol, which further corroborated the strong binding. During 100 ns of simulation, the ligand binds to the active sites of these proteins through the H-bonds at Ile107 of LasI, Tyr47 of LasR, and Leu57 of BswR. In addition, the root-mean-square deviation values of the ligand-protein complex are within the appropriate range of less than 5 Å. Absorption, Distribution, Metabolism, Excretion, and Toxicity analysis confirmed that carvacrol has the most negligible toxicity to mammalian cells. Hence, this finding is the first report to show that carvacrol can inhibit the <i>Pseudomonas aeruginosa</i> biofilms.</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":"142680845","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}
引用次数: 0
What in Earth? Analyses of Canadian soil populations of Aspergillus fumigatus. 地球上有什么?加拿大土壤曲霉菌群分析。
IF 1.8 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 Epub Date: 2024-10-15 DOI: 10.1139/cjm-2024-0083
Greg Korfanty, Arshia Kazerouni, Mykaelah Dixon, Micheala Trajkovski, Paola Gomez, Jianping Xu
{"title":"What in Earth? Analyses of Canadian soil populations of <i>Aspergillus fumigatus</i>.","authors":"Greg Korfanty, Arshia Kazerouni, Mykaelah Dixon, Micheala Trajkovski, Paola Gomez, Jianping Xu","doi":"10.1139/cjm-2024-0083","DOIUrl":"10.1139/cjm-2024-0083","url":null,"abstract":"<p><p><i>Aspergillus fumigatus</i> is a globally distributed mold and a major cause of opportunistic infections in humans. Because most infections are from environmental exposure, it is critical to understand environmental populations of <i>A. fumigatus</i>. Soil is a major ecological niche for <i>A. fumigatus</i>. Here, we analyzed 748 soil isolates from 21 locations in six provinces and one territory in Canada. All isolates were genotyped using nine microsatellite markers. Due to small sample size and/or close proximities for some local samples, these isolates were grouped into 16 local geographic and ecological populations. Our results indicated high allelic and genotypic diversities within most local and provincial populations. Interestingly, low but statistically significant genetic differentiations were found among geographic populations within Canada, with relatively similar proportions of strains and genotypes belonging to two large genetic clusters. In Hamilton, Ontario, and Vancouver, BC, where two and three ecological populations were analyzed, respectively, we found limited genetic difference among them. Most local and provincial populations showed evidence of both clonality and recombination, with no population showing random recombination. Of the 748 soil isolates analyzed here, two were resistant to triazole antifungals. We discuss the implications of our results to the evolution and epidemiology of <i>A. fumigatus</i>.</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":"142458630","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}
引用次数: 0
AcsS inhibits the hemolytic activity and thermostable direct hemolysin (TDH) gene expression in Vibrio parahaemolyticus. AcsS 可抑制副溶血弧菌的溶血活性和热稳定直接溶血素(TDH)基因的表达。
IF 1.8 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 Epub Date: 2024-11-13 DOI: 10.1139/cjm-2024-0114
Bin Ni, Zhukang Tian, Jingyang Chang, Yining Zhou, Xue Li, Miaomiao Zhang, Wanpeng Li, Nan Zhang, Xi Luo, Yiquan Zhang, Renfei Lu
{"title":"AcsS inhibits the hemolytic activity and thermostable direct hemolysin (TDH) gene expression in <i>Vibrio parahaemolyticus</i>.","authors":"Bin Ni, Zhukang Tian, Jingyang Chang, Yining Zhou, Xue Li, Miaomiao Zhang, Wanpeng Li, Nan Zhang, Xi Luo, Yiquan Zhang, Renfei Lu","doi":"10.1139/cjm-2024-0114","DOIUrl":"10.1139/cjm-2024-0114","url":null,"abstract":"<p><p><i>Vibrio parahaemolyticus</i> produces a key virulent factor known as thermostable direct hemolysin (TDH). TDH exhibits diverse biological activities, including hemolytic activity. The β-type hemolysis observed on Wagatsuma agar due to TDH is recognized as the Kanagawa phenomenon (KP). The <i>tdh2</i> gene is primarily responsible for TDH production and the associated KP. AcsS was originally identified as an activator of swimming and swarming motility in <i>V. parahaemolyticus</i>. However, its potential roles in other cellular pathways remain unclear. In this study, we investigated the regulatory effects of AcsS on the hemolytic activity and <i>tdh2</i> expression in <i>V. parahaemolyticus</i> using phenotypic tests for KP, quantitative real-time polymerase chain reaction, LacZ fusion, and electrophoretic mobility shift assays. The data showed that <i>V. parahaemolyticus</i> hemolytic activity and <i>tdh2</i> transcription were under the negative control of AcsS. Additionally, in-vitro binding assays revealed that His-AcsS could not bind to the regulatory DNA region of <i>tdh2</i>. However, overexpression of AcsS in an <i>Escherichia coli</i> strain suppressed the expression of <i>tdh2</i>. Collectively, these results suggested that AcsS suppresses the hemolytic activity of <i>V. parahaemolyticus</i> through the downregulation of <i>tdh2</i> transcription. The data enhanced our understanding of the regulatory networks governing <i>tdh2</i> expression and the roles of AcsS in this bacterium.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-6"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142615299","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}
引用次数: 0
Genomic characterization of pathotype diversity and drug resistance among generic Escherichia coli isolated from broiler chickens in Canada. 加拿大肉鸡分离的通用大肠杆菌的病原多样性和耐药性的基因组特征。
IF 1.8 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 DOI: 10.1139/cjm-2024-0209
Rhiannon L Wallace, Shawn Hoogstra, David Mahoney, Mark Lubberts, Richard Reid-Smith, Tara Signorelli, James Robertson, Shannon H C Eagle, Emil Jurga, John Nash, Edward Topp, Catherine Carrillo
{"title":"Genomic characterization of pathotype diversity and drug resistance among generic <i>Escherichia coli</i> isolated from broiler chickens in Canada.","authors":"Rhiannon L Wallace, Shawn Hoogstra, David Mahoney, Mark Lubberts, Richard Reid-Smith, Tara Signorelli, James Robertson, Shannon H C Eagle, Emil Jurga, John Nash, Edward Topp, Catherine Carrillo","doi":"10.1139/cjm-2024-0209","DOIUrl":"10.1139/cjm-2024-0209","url":null,"abstract":"<p><p><i>Escherichia coli</i> is a Gram-negative bacterium that is ubiquitous in animals and humans, with some strains capable of causing disease. The aim of this study was to perform a comparative genomic analysis of 2732 generic <i>E. coli</i> isolates that were recovered from poultry samples collected from six regions in Canada as part of the National Microbiological Baseline study in Broiler Chicken. Isolates were subjected to whole genome sequencing and a subset (1122/2732) were tested for phenotypic resistance to 15 antimicrobials. These <i>E. coli</i> isolates were highly diverse, representing 376 serotypes, 236 sequence types and 21 pathotypes, of which 19 were hybrid pathotypes. A high concordance (>85%) between resistance phenotype and the presence of antimicrobial resistance genes and point mutations (resistance determinants) was observed for 13/15 antimicrobials. Over 95% of the β-lactam, fluoroquinolone, and phenicol resistance genes were predicted to be plasmid-borne. The number of resistance determinants per genome was highest in Quebec, while resistance genes associated with β-lactam resistance were more frequently detected in isolates from British Columbia. Generic <i>E. coli</i> in Canadian poultry are highly diverse, can carry pathotype-associated virulence factors and resistance determinants of clinical significance with a risk of emerging into pathogenic strains.</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":"143000704","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}
引用次数: 0
Molecular epidemiology and in silico prediction of ciprofloxacin resistance in Salmonella enterica in Canada, 2017-2022. 2017-2022年加拿大肠道沙门氏菌环丙沙星耐药的分子流行病学和计算机预测
IF 1.8 4区 生物学
Canadian journal of microbiology Pub Date : 2025-01-01 DOI: 10.1139/cjm-2024-0118
MacKenzie A P Wilke, Ketna Mistry, David Thumbi, Xiao Rui Li, Audrey Charlebois, Ashley C Cormier, Katrina Mickanuck, Brent P Avery, Colleen Murphy, Anne E Deckert, Ashley Kearney, Jennifer Campbell, Sara Christianson, David C 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 R Mulvey, Carolee A Carson, Richard J Reid-Smith, Amrita Bharat
{"title":"Molecular epidemiology and in silico prediction of ciprofloxacin resistance in <i>Salmonella enterica</i> in Canada, 2017-2022.","authors":"MacKenzie A P Wilke, Ketna Mistry, David Thumbi, Xiao Rui Li, Audrey Charlebois, Ashley C Cormier, Katrina Mickanuck, Brent P Avery, Colleen Murphy, Anne E Deckert, Ashley Kearney, Jennifer Campbell, Sara Christianson, David C 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 R Mulvey, Carolee A Carson, Richard J Reid-Smith, Amrita Bharat","doi":"10.1139/cjm-2024-0118","DOIUrl":"10.1139/cjm-2024-0118","url":null,"abstract":"<p><p>Ciprofloxacin is important for treatment of severe or invasive <i>Salmonella</i> 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 <i>Salmonella</i> 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 <i>Salmonella enterica</i> 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 <i>gyrA</i> (especially S83F and D87N/D87Y) and the <i>qnrB19</i> 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":"1-8"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","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}
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