Canadian journal of microbiology最新文献

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 2321 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.

Community-associated Clostridioides difficile 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 C. difficile 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 C. difficile, 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.

Streptococcus suis and Glaesserella parasuis 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 G. parasuis could impact S. suis growth dynamics. We compared phenotypic properties of a clinical S. suis 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 G. parasuis 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 G. parasuis increased planktonic or sessile cell counts. Our study suggests that increased temperature in the host may be an important factor in understanding S. suis disease development.

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.

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.

The use of Trichoderma in agriculture as both a biocontrol agent and biofertilizer hinges on its ability to colonize the rhizosphere, promote plant growth, endure adverse environments, compete for space and nutrients, and produce enzymes and secondary metabolites to mycoparasitize and infect other fungus. In humans, Trichoderma exhibits the capacity to infect various bodily tissues, leading to Trichodermosis. There has been a notable increase in cases ranging from superficial to fatal, invasive, and disseminated infections, particularly among immunocompromised individuals. Trichoderma species employ diverse strategies to colonize and survive in various environments, infecting phytopathogens; however, the mechanisms and virulence factors contributing to human infections remain poorly understood. In this mini review, we provide a brief overview and contextualization of the virulence mechanisms employed by Trichoderma in parasitizing other fungi, as well as those implicated in modulating plant immunity and inducing human infections. Furthermore, we discuss the similarity of these virulence factors capable of modulating the mammalian immune system and their potential implications for human infection.

Rhizobia are soil-dwelling proteobacteria that can enter into symbiotic nitrogen-fixing relationships with compatible leguminous plants. Taxonomically, rhizobia are divided into alpha-rhizobia, which belong to the class Alpharoteobacteria, and beta-rhizobia, which belong to the class Betaproteobacteria. To date, all bona fide alpha-rhizobia belong to the order Hyphomicrobiales. However, a recent study suggested that Sphingomonas sediminicola DSM 18106^T is also a rhizobium and is capable of nodulating pea plants (Pisum sativum), which would expand the known taxonomic distribution of alpha-rhizobia to include the order Sphingomonadales. Here, we attempted to replicate the results of that previous study. Resequencing and computational analysis of the genome of S. sediminicola DSM 18106^T failed to identify genes encoding proteins involved in legume nodulation or nitrogen fixation. In addition, experimental plant assays indicated that S. sediminicola DSM 18106^T is unable to nodulate the two cultivars of pea tested in our study, unlike the rhizobium Rhizobium johnstonii 3841^T. Taken together, and in contrast to the previous study, these results suggest that S. sediminicola DSM 18106^T is not capable of inducing root nodule formation on pea, meaning that the taxonomic distribution of all known alpha-rhizobia remains limited to the class Hyphomicrobiales.

On solid substrates, biofilms develop rich wrinkle morphologies during its growth. Based on the thin film buckling theory, we established a local three-dimensional biofilm/substrate buckling model, and explored the effects of mechanical forces, elastic modulus of the substrate, and biofilm thickness on the wrinkle morphology. We simulated the wrinkle evolution in various patterns of Bacillus subtilis biofilm growing on agar substrates with different stiffness and found that the biofilm wrinkling process is the process of internal energy release. The stiffness of the substrate changes the wrinkling time of the biofilm; The biofilm wrinkle morphology (patterns II, III, and IV) U_internal and U_internal/U₀ decrease with nutrient consumption, and the biofilm evolves towards lower energy consumption. In the early stages of biofilm growth (patterns I, II, and III), the harder the agar substrate, the larger the U_friction and U_friction/U₀, which is less conducive to biofilm expansion.

DNA synthesis and assembly techniques have enabled the creation of validated and standardized DNA parts, used for producing proteins, enzymes, and small molecules. However, most DNA parts are governed by Material Transfer Agreements, which restrict sharing and reuse for commercial purposes even in the absence of patents, bottlenecking innovation. DNA synthesis, crucial for producing new parts, also remains expensive and therefore inaccessible to most researchers. With the breakneck pace of digital innovations for designing and learning from biology, a new and more open approach to the physical building and testing of biology is needed. We propose the establishment of an Open Bio Research Alliance, to create and distribute open collections of DNA and other biological parts, combined with regulated and affordable DNA synthesis services. Focusing on Canada's bioeconomy, establishing domestic DNA synthesis infrastructure would not only secure global competitiveness in engineering biology, but also safeguard biosecurity and national sovereignty over critical resources. By harnessing and supporting existing lab automation resources, the Alliance will also help scale the building and testing of engineered biological systems. Leveraging these tools and strategies, Canada is well-positioned to lead the world in open and innovative biotechnology, paving the way for a thriving bioeconomy.