Canadian journal of microbiology最新文献

{"title":"Comparative mitogenomics of <i>Leptographium procerum, Leptographium terebrantis</i>, and <i>Leptographium wingfieldii</i>, an invasive fungal species in Canadian forests.","authors":"Abdullah Zubaer, Alvan Wai, Georg Hausner","doi":"10.1139/cjm-2024-0179","DOIUrl":"10.1139/cjm-2024-0179","url":null,"abstract":"<p><p><i>Leptographium wingfieldii</i> is a fungal associate of <i>Tomicus piniperda</i> (the pine shoot beetle) and pathogen of pines and this species is an agent of blue stain in sapwood on infected trees. This fungus was first reported from Europe and has been recently introduced to Canadian forests. Ten new mitogenomes have been sequenced and characterized, including seven strains of <i>L. wingfieldii</i>, two strains of <i>L. procerum</i> and one strain of <i>L. terebrantis</i>. The data were combined with other members of the Ophiostomatales collected from NCBI to gain more insight into the genetic diversity, evolution, and systematics of these fungi. The size of the studied mitogenomes of <i>Leptographium</i> species ranged from 41 to 126 kb with the number of potential mobile introns embedded within these mitogenomes ranging from 13 to 45. These data show that introns generate genetic diversity and confirms the contribution of mobile introns in genome expansion in Ophiostomatales fungi. This study also uncovered complex intron arrangements (twintrons) suggesting the potential of mobile introns generating complex ribozymes that may have implications in gene regulation.</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":"142817378","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":"High-throughput sequencing reveals microbial community dynamics in two treatment systems for oil field-produced water.","authors":"Yi Li, Shuo Han, Xiangwei He","doi":"10.1139/cjm-2024-0202","DOIUrl":"10.1139/cjm-2024-0202","url":null,"abstract":"<p><p>Petroleum-associated water harbors diverse microbial communities, including hydrocarbon-degrading bacteria, sulfate-reducing bacteria, and methanogenic archaea. The growth and metabolism of these organisms, as well as their community composition, can affect various aspects of oil field development and oil produced water treatment. In this study, Illumina-based 16S rRNA gene sequencing was used to analyze the microbial community structures of oilfield produced water processed at two treatment stations and subjected to different treatment protocols. Significant differences in microbial community α-diversity and richness resulted from the different treatment protocols. The treatment of oil produced water effectively reduced the oil content, accompanied by the a reduction in Desulfobacterota. Proteobacteria was the dominant phylum in oil produced water; its core presence, along with Patescibacteria and Desulfobacterota, was identified in a co-occurrence network analysis of the microbial community. Redundancy analysis showed significant positive correlations between microbial community diversity and the oil and suspended solids contents of the oil produced water, highlighting the role of treatment protocols in shaping both microbial composition and water characteristics. Thus, this study provides potential insights into the processes of souring in oil fields and contributes to the theoretical understanding of oil-produced water treatment, which may inform future optimization of treatment protocols.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-11"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143974872","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":"Note of appreciation.","authors":"","doi":"10.1139/cjm-2024-0228","DOIUrl":"https://doi.org/10.1139/cjm-2024-0228","url":null,"abstract":"","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":"71 ","pages":"1"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000717","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":"Mechanisms and implications of phenotypic switching in bacterial pathogens.","authors":"Alexander Stephen Byrne, Nathalie Bissonnette, Kapil Tahlan","doi":"10.1139/cjm-2024-0116","DOIUrl":"10.1139/cjm-2024-0116","url":null,"abstract":"<p><p>Bacteria encounter various stressful conditions within a variety of dynamic environments, which they must overcome for survival. One way they achieve this is by developing phenotypic heterogeneity to introduce diversity within their population. Such distinct subpopulations can arise through endogenous fluctuations in regulatory components, wherein bacteria can express diverse phenotypes and switch between them, sometimes in a heritable and reversible manner. This switching may also lead to antigenic variation, enabling pathogenic bacteria to evade the host immune response. Therefore, phenotypic heterogeneity plays a significant role in microbial pathogenesis, immune evasion, antibiotic resistance, host niche tissue establishment, and environmental persistence. This heterogeneity can result from stochastic and responsive switches, as well as various genetic and epigenetic mechanisms. The development of phenotypic heterogeneity may create clonal populations that differ in their level of virulence, contribute to the formation of biofilms, and allow for antibiotic persistence within select morphological variants. This review delves into the current understanding of the molecular switching mechanisms underlying phenotypic heterogeneity, highlighting their roles in establishing infections caused by select bacterial pathogens.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-19"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370976","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":"Surveillance of <i>Clostridioides difficile</i> in Canadian retail meat and genomic linkages to community-associated human clinical infections in Canada.","authors":"Paula E Pidsadny, Tim Du, Romeo Hizon, Sean Ahmed, Derek Tan, George G Zhanel, Denice C Bay, Richard J Reid-Smith, Audrey Charlebois, George R Golding","doi":"10.1139/cjm-2024-0193","DOIUrl":"10.1139/cjm-2024-0193","url":null,"abstract":"<p><p>Community-associated <i>Clostridioides difficile</i> infections (CA-CDI) remain a concern in Canada, comprising a quarter of cases previously reported through the Canadian Nosocomial Infection Surveillance Program. Previous Canadian studies have reported toxigenic <i>C. difficile</i> isolated from Canadian retail meat, suggesting that it may be a source of exposure for CA-CDI in Canada. In this study, 3/219 (1.4%) of retail pork and 0/99 (0%) of retail beef samples tested positive for toxigenic <i>C. difficile</i>, which were molecularly characterized by PCR ribotyping and whole-genome sequencing. All three isolates were obtained from pork and belonged to sequence types (STs)/ribotypes (RTs) that have previously been isolated from human clinical CA-CDI cases in Canada: ST1/RT027, ST8/RT002, and ST10/RT015. Retail meat isolates were susceptible to the antimicrobials tested, save one isolate with intermediate resistance to clindamycin. Genomic comparison to Canadian human clinical CA-CDI isolates with the same corresponding ST/RT types showed two of the three pork isolates clustered with CA-CDI isolates via core-genome multilocus sequencing typing, with single nucleotide variant (SNV) analysis showing further genomic relatedness of 2-11 SNVs. Retail meat may therefore be a low source of CA-CDI exposure in Canada, with the potential for foodborne transmission of select clones.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-7"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143498621","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":"Investigating the occurrence of antimicrobial resistance in the environment in Canada: a scoping review.","authors":"Manuel Pérez Maldonado, Daniel Ofori-Darko, Vanessa Nichols, Jessica French, Kelsey Spence, Richard J Reid-Smith, E Jane Parmley","doi":"10.1139/cjm-2024-0189","DOIUrl":"10.1139/cjm-2024-0189","url":null,"abstract":"<p><p>Antimicrobial resistance is an environmental, agricultural, and public health problem that is impacting the health of humans and animals. The role of the environment as a source of and transmission pathway for antibiotic resistant bacteria and antibiotic resistance genes is a topic of increasing interest that, to date, has received limited attention. This study aimed to describe the sources and possible pathways contributing to antimicrobial resistance dissemination through bioaerosols, water, and soil in Canada using a scoping review methodology and systems thinking approach. A systems map was created to describe the occurrence and relationships between sources and pathways for antimicrobial resistance dissemination through water, soil, and bioaerosols. The map guided the development of the scoping review protocol, specifically the keywords searched and what data were extracted from the included studies. In total, 103 studies of antimicrobial resistance in water, 67 in soil, and 12 in air were identified. Studies to detect the presence of antimicrobial resistance genes have mainly been conducted at wastewater treatment plants and commercial animal livestock facilities. We also identified elements in the systems map with little or no data available (e.g., retail) that need to be investigated further to have a better understanding of antimicrobial resistance dissemination through different Canadian environments.</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":"143966425","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>Streptococcus suis</i> serovar 9 responses to elevated temperature and co-culture with <i>Glaesserella parasuis</i>.","authors":"B S Spoja, A R Bujold, J I MacInnes, N Ricker","doi":"10.1139/cjm-2024-0180","DOIUrl":"10.1139/cjm-2024-0180","url":null,"abstract":"<p><p><i>Streptococcus suis</i> and <i>Glaesserella parasuis</i> are commensal organisms that can shift from a benign to pathogenic state and cause severe disease in swine. We hypothesized that a change in host temperature and/or interactions with <i>G. parasuis</i> could impact <i>S. suis</i> growth dynamics. We compared phenotypic properties of a clinical <i>S. suis</i> serovar 9 strain (SS9C) with clinical serovar 2 and healthy serovar 9 isolates grown at 37 and 41 °C. We further investigated how co-culturing with <i>G. parasuis</i> affected biofilm formation of SS9C. Crystal violet staining indicated that SS9C produced significantly more biofilm than the other strains when grown at 37 °C; this difference was amplified at 41 °C. However, cell counts did not increase at the higher temperature. Biofilms of SS9C at 37 and 41 °C were unaffected by DNase I digestion, while other strains were both susceptible at 41 °C. All biofilms were susceptible to proteinase K and α-amylase digestion at both temperatures. We showed that growth at 41 °C increased biofilm formation and shifted the phenotype of SS9C; however, neither increased temperature nor co-culture with <i>G. parasuis</i> increased planktonic or sessile cell counts. Our study suggests that increased temperature in the host may be an important factor in understanding <i>S. suis</i> disease development.</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":"143972444","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":"Microbiome profiling suggests novel endosymbiont associations of insect pests of stored grain.","authors":"Janice Fajardo, Brian Harrison, Vincent A D Hervet, Matthew G Bakker","doi":"10.1139/cjm-2024-0095","DOIUrl":"10.1139/cjm-2024-0095","url":null,"abstract":"<p><p>Many arthropods, including economically important pests of stored grains, host intracellular bacterial symbionts. These symbionts can have diverse impacts on host morphology, stress tolerance, and reproductive success. The ability to rapidly determine the infection status of host insects and the identity of intracellular symbionts, if present, is vital to understanding the biology and ecology of these organisms. We used a microbiome profiling method based on amplicon sequencing to rapidly screen 35 captive insect colonies. This method effectively revealed single and mixed infections by intracellular bacterial symbionts, as well as the presence or absence of a dominant symbiont, when that was the case. Because no a priori decisions are required about probable host-symbiont pairing, this method is able to quickly identify novel associations. This work highlights the frequency of endosymbionts, indicates some unexpected pairings that should be investigated further, such as dominant bacterial taxa that are not among the canonical genera of endosymbionts, and reveals different colonies of the same host insect species that differ in the presence and identity of endosymbiotic bacteria.</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":"142674980","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":"Longitudinal screening of retail milk from Canadian provinces reveals no detections of influenza A virus RNA (April-July 2024): leveraging a newly established pan-Canadian network for responding to emerging viruses.","authors":"Hannah L Wallace, Jordan Wight, Mariana Baz, Barbara Dowding, Louis Flamand, Tom Hobman, François Jean, Jeffrey B Joy, Andrew S Lang, Sonya MacParland, Craig McCormick, Ryan Noyce, Rodney S Russell, Selena M Sagan, Jumari Snyman, Gabriela J Rzeszutek, Mustafa S Jafri, Isaac Bogoch, Jason Kindrachuk, Angela L Rasmussen","doi":"10.1139/cjm-2024-0120","DOIUrl":"10.1139/cjm-2024-0120","url":null,"abstract":"<p><p>Highly pathogenic avian influenza (HPAI) H5N1 has caused the deaths of more than 100 million birds since 2021, and human cases since 1997 have been associated with significant morbidity and mortality. Given recent detections of HPAI H5N1 in dairy cattle and H5N1 RNA detections in pasteurized retail milk in the United States, we established the pan-Canadian Milk Network in April 2024. Through our network of collaborators from across Canada, retail milk was procured longitudinally, approximately every 2 weeks, and sent to a central laboratory to test for the presence of influenza A virus RNA. Between 29 April and 17 July 2024, we tested 109 retail milk samples from all 10 Canadian provinces (NL, NS, PEI, NB, QC, ON, MB, SK, AB, and BC). All samples tested negative for influenza A virus RNA. This nationwide initiative was established for rapid retail milk screening as per the earliest reports of similar undertakings in the United States. Our independent testing results have aligned with reporting from federal retail milk testing initiatives. Despite no known HPAI infections of dairy cattle in Canada to date, H5N1 poses a significant threat to the health of both humans and other animals. By performing routine surveillance of retail milk on a national scale, we have shown that academic networks and initiatives can rapidly establish nationwide emerging infectious disease surveillance that is cost-effective, standardized, scalable, and easily accessible. Our network can serve as an early detection system to help inform containment and mitigation activities if positive samples are identified and can be readily reactivated should HPAI H5N1 or other emerging zoonotic viruses be identified in agricultural or livestock settings, including Canadian dairy cattle.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-7"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142342147","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 <i>Salmonella</i>.","authors":"Benjamin M Hetman, David L Pearl, Richard Reid-Smith, E Jane Parmley, Eduardo N Taboada","doi":"10.1139/cjm-2024-0090","DOIUrl":"10.1139/cjm-2024-0090","url":null,"abstract":"<p><p>Whole-genome sequence-based surveillance of bacteria for determinants of antimicrobial resistance (AMR) 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 <i>Salmonella</i> Heidelberg and <i>S.</i> 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 AMR determinants in bacteria sampled from food products and animals related to food production.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-17"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","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}