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- Balasubramaniam, Thiropa1
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- Blais, Burton W1
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- OPEN ACCESSIn some species where males make no direct contribution to a female’s lifetime reproductive success, females choose mates based on the indirect benefits manifested in their offspring. One trait that may be subject to this sexual selection is immunocompetence (the ability to mount an immune response following exposure to pathogens); however, the results of previous work on its link to male attractiveness have been ambiguous. Herein we examine the life history consequences of mating with males with a history of failure or success in reproductive competitions in Drosophila melanogaster. By examining egg-to-adult survival, body weights, and bacterial loads of offspring reared in either the absence or presence of a bacterial pathogen, we were able to examine whether sire reproductive success was associated with their offsprings’ ability to respond to an immunological challenge and other life history traits. Our results are partially consistent with the predictions of the “immunocompetence handicap hypothesis”: competitively successful males (“studs”) sire male offspring that are better able to handle an immunological challenge than those sired by competitively unsuccessful males (“duds”). However, our assay also revealed the opposite pattern in female offspring, suggestive of the complicating presence of alleles with sexually antagonistic effects on the expression of this important life history trait.
- OPEN ACCESSDeadly outbreaks and illnesses due to Shiga toxin-producing Escherichia coli (STEC) occur worldwide; however, the cultivation methods required for adequate monitoring and traceback investigations are inefficient at best. Detection of STEC relies heavily on enrichment; yet no standard media or protocols exist. Furthermore, whether enrichment may bias detection of multiple STEC serogroups from complex samples is unknown. Thus, 14 STEC strains of serogroups O157 and the top six non-O157s (O26, O45, O103, O111, O121, and O145) were enriched in pairs for 6–78 h in broth and evaluated by quantitative polymerase chain reaction (qPCR). Here we show that a conventional 6-h enrichment protocol did not result in intra-species culture bias for the isolates tested. However, subsequent enrichments often produced biased cultures, with differences in the qPCR gene copy number ≥2 log10 apparent in 12%, 38%, and 52% of competitions after 30, 54, and 78 h of consecutive enrichments, respectively. Some strains were able to prevail and (or) out-compete the opponent strain in 100% of competitions. Our results suggest that culture bias should be considered and (or) evaluated further due to the potential implications during routine pathogen screening and outbreak investigations.
- OPEN ACCESSA novel Brachyspira emerged in 2009 and has since become a production-limiting pathogen of pigs in North America. The name “Brachyspira hampsonii” has been proposed for this novel taxon. “Brachyspira hampsonii” is divided into two phylogenetically distinct clades based on the sequence of the NADH-oxidase (nox) gene, although the clinical disease associated with clades I and II is indistinguishable and phenotypic characteristics that discriminate the clades have not been determined. The objectives of the current study were to enhance the description of the provisional species “B. hampsonii” with biochemical profiles and morphometric data from isolates affecting Canadian swine and to investigate potentially diagnostically informative characteristics for this emerging pathogen. Biochemical profiles of isolates from different commercial swine barns in Western Canada showed that biochemical profiles were insufficient to distinguish “B. hampsonii” clades I and II from each other or from other pathogenic Brachyspira. Hippurate hydrolysis, previously reported as uniformly negative in “B. hampsonii,” was variable among Canadian isolates. Spirochete dimensions and flagella numbers for “B. hampsonii” overlapped with other Brachyspira species. Taken together, these results indicate that nox gene sequencing remains a preferred method for identification and discrimination of “B. hampsonii” from other pig-associated Brachyspira spp.
- OPEN ACCESSBacterial endophytes are thought to enter plants either through pre-existing openings in plant tissues or by creating openings by hydrolyzing major plant cell wall components. A lodgepole endophyte, Paenibacillus polymyxa P2b-2R, consistently formed endophytic colonies when inoculated in diverse plant hosts, viz., lodgepole pine, western red cedar, corn, canola, and tomato. We were interested to know, whether or not this bacterial strain possesses enzymes that can hydrolyze three major plant cell wall components namely cellulose, xylan, and pectin to facilitate entrance into the host plants. Using a BIOLOG assay, we also tested this bacterial strain’s ability to utilize carbon sources that might facilitate its entrance and hence its survival inside host plants. Paenibacillus polymyxa P2b-2R hydrolyzed sodium carboxymethylcellulose, beechwood xylan, and sodium polypectate and utilized 39 of the 95 carbon sources (41%) tested. Of the 39 carbon substrates oxidized by P2b-2R, the “carbohydrates” group represents the largest source of utilizable carbon (23 out of 39). Thus, it can be concluded that P. polymyxa P2b-2R is able to degrade major cell wall components (cellulose, xylan, and pectin) and utilize some of the available carbon substrates, possibly to gain entry and survive inside the plant and form endophytic colonies thereafter.
- OPEN ACCESSAspects of Canada’s health regulatory system are currently being reviewed. This is timely, as the regulation and definition of drugs, foods, and natural health products (NHPs) is in need of revision to facilitate greater transparency and less ambiguity. A number of studies have illustrated the importance of a nutritious diet to prevent and manage chronic disease. Therefore, legislation surrounding food health claims needs to be adjusted so that it is more informative for disease prevention and, in some cases, treatment. Canada is modernizing the regulation of self-care products, under which NHPs, including probiotic products, are listed. With the growing appreciation for the role that microbes play in human health and the recognition that many foods, including those containing probiotic organisms, can prevent or mitigate disease, this provides an opportunity to reassess regulatory categories.
- OPEN ACCESS
- Claire N. Freeman,
- Lena Scriver,
- Kara D. Neudorf,
- Lisbeth Truelstrup Hansen,
- Rob C. Jamieson, and
- Christopher K. Yost
Wastewater treatment plants (WWTPs) have been identified as hotspots for antimicrobial resistance genes (ARGs) and thus represent a critical point where patterns in ARG abundances can be monitored prior to their release into the environment. The aim of the current study was to measure the impact of the release of the final treated effluent (FE) on the abundance of ARGs in the receiving water of a recently upgraded WWTP in the Canadian prairies. Sample nutrient content (phosphorous and nitrogen species) was measured as a proxy for WWTP functional performance, and quantitative PCR (qPCR) was used to measure the abundance of eight ARGs, the intI1 gene associated with class I integrons, and the 16S rRNA gene. The genes ermB, sul1, intI1, blaCTX-M, qnrS, and tetO all had higher abundances downstream of the WWTP, consistent with the genes with highest abundance in the FE. These findings are consistent with the increasing evidence suggesting that human activity affects the abundances of ARGs in the environment. Although the degree of risk associated with releasing ARGs into the environment is still unclear, understanding the environmental dimension of this threat will help develop informed management policies to reduce the spread of antibiotic resistance and protect public health. - OPEN ACCESSMercury (Hg) is a global pollutant emitted primarily as gaseous Hg0 that is deposited in aquatic and terrestrial ecosystems following its oxidation to HgII. From that point, microbes play a key role in determining Hg’s fate in the environment by participating in sequestration, oxidation, reduction, and methylation reactions. A wide diversity of chemotrophic and phototrophic microbes occupying oxic and anoxic habitats are known to participate directly in Hg cycling. Over the last few years, new findings have come to light that have greatly improved our mechanistic understanding of microbe-mediated Hg cycling pathways in the environment. In this review, we summarize recent advances in microbially mediated Hg cycling and take the opportunity to compare the relatively well-studied chemotrophic pathways to poorly understood phototrophic pathways. We present how the use of genomic and analytical tools can be used to understand Hg transformations and the physiological context of recently discovered cometabolic Hg transformations supported in anaerobes and phototrophs. Finally, we propose a conceptual framework that emphasizes the role that phototrophs play in environmental Hg redox cycling and the importance of better characterizing such pathways in the face of the environmental changes currently underway.
- OPEN ACCESSFish, amphibians, and reptiles exhibit temperature-dependent ranaviral disease. We performed an experimental infection at four different environmental temperatures (16, 22, 28, and 34 °C) to investigate the effect of temperature on ranaviral infection in Krefft’s turtle (Emydura macquarii krefftii). Infection rates and viral loads were determined by quantitative polymerase chain reaction to detect ranaviral DNA in liver samples at 21 d postexposure. The rate of infection differed across the temperature treatment groups. Infection rates were 44%, 90%, 60%, and 10% for the 16, 22, 28, and 34 °C temperature groups, respectively. Highest viral load was observed in the 28 °C temperature group, and there was a statistically significant difference in viral load between the 16 and 28 °C temperature groups (p = 0.027). Based on the results of this study, the temperature of maximal infection rate for ranaviral infection in Krefft’s river turtles is estimated to be 23.2 °C (SD = 4.5). The findings of this study can inform management decisions in terms of disease control and treatment and form a platform for modelling disease outbreaks.
- OPEN ACCESSRanaviruses are large nucleocytoplasmic DNA viruses that infect ectothermic vertebrates. Here we report the results of a scientometric analysis of the field of ranavirology for the last 10 years. Using bibliometric tools we analyse trends, identify top publications and journals, and visualise the ranavirus collaboration landscape. The Web of Science core collection contains 545 ranavirus-related publications from 2010 to 2019, with more publications produced every year and a total of 6830 citations. Research output is primarily driven by the United States and People’s Republic of China, who together account for more than 60% of ranavirus publications. We also observed a positive correlation between the average number of co-authors on ranavirus publications and the year of publication, indicating that overall collaboration is increasing. A keyword analysis of ranavirus publications from 2010 to 2019 reveals several areas of research interest including; ecology, immunology, virology/molecular biology, genetics, ichthyology, and herpetology. While ranavirus research is conducted globally, relatively few publications have co-authors from both European and Asian countries, possibly because closer countries (geographical distance) are more likely to share co-authors. To this end, efforts should be made to foster collaborations across geopolitical and cultural boundaries, especially between countries with shared research interests as ultimately, understanding global pathogens, like ranaviruses, will require global collaboration.
- OPEN ACCESS
- Ashley L. Cooper,
- Cassandra Carter,
- Hana McLeod,
- Marie Wright,
- Prithika Sritharan,
- Sandeep Tamber,
- Alex Wong,
- Catherine D. Carrillo, and
- Burton W. Blais
Bacterial carbapenem resistance is a major public health concern since these antimicrobials are often the last resort to treat serious human infections. To evaluate methodologies for detection of carbapenem resistance, carbapenem-tolerant bacteria were isolated from wastewater treatment plants in Toronto, Ottawa, and Arnprior, Ontario. A total of 135 carbapenem-tolerant bacteria were recovered. Polymerase chain reaction (PCR) indicated the presence of carbapenem hydrolysing enzymes KPC (n = 10), GES (n = 5), VIM (n = 7), and IMP (n = 1), and β-lactamases TEM (n = 7), PER (n = 1), and OXA-variants (n = 16). A subset of 46 isolates were sequenced and analysed using ResFinder and CARD-RGI. Both programs detected carbapenem resistance genes in 35 sequenced isolates and antimicrobial resistance genes (ARGs) conferring resistance to multiple class of other antibiotics. Where β-lactamase resistance genes were not initially identified, lowering the thresholds for ARG detection enabled identification of closely related β-lactamases. However, no known carbapenem resistance genes were found in seven sequenced Pseudomonas spp. isolates. Also of note was a multi-drug-resistant Klebsiella pneumoniae isolate from Ottawa, which harboured resistance to seven antimicrobial classes including β-lactams. These results highlight the diversity of genes encoding carbapenem resistance in Ontario and the utility of whole genome sequencing over PCR for ARG detection where resistance may result from an assortment of genes. - OPEN ACCESSSalt marshes are ecosystems of significant ecological importance for coastal stability and fundamental roles in marine ecosystems. Salt marshes are declining due to anthropogenic and natural causes including sea level rise. Coastal restoration efforts have increased worldwide, but many fail in long-term coastal stability. We used a naturally occurring arbuscular mycorrhizal fungus (AMF) to test whether survival and early growth of the salt marsh grass Sporobolus pumilus (formerly Spartina patens) improved under simulated salt marsh conditions. Using a tidal mesocosm bench, we grew inoculated plants with varying AMF treatments under simulated tidal regimes to determine if AMF could aid in establishment of healthy Sporobolus communities. Rhizome-derived S. pumilus had greater survival and grew faster than seed-derived plants. Plants inoculated with propagated AMF consistently outperformed both sterile and native sediment controls in terms of plant survival and growth. Use of rhizome-derived Sporobolus inoculated with propagated Funneliformis geosporum showed the most promise in producing successful plant populations for salt marsh restoration. This may be due to plant life stage and improved plant nutrient status, allowing rhizome-derived plants to grow more quickly than seed-derived plants. Using these plants in future large-scale restoration may increase re-establishment of salt marsh ecosystems.
- OPEN ACCESS
- Yannan Huang,
- Lindsay Johnston,
- Ana Parra,
- Crystal Sweeney,
- Emalie Hayes,
- Lisbeth Truelstrup Hansen,
- Graham Gagnon,
- Amina Stoddart, and
- Rob Jamieson
Wastewater-based surveillance methods have been implemented in several countries as a tool for monitoring SARS-CoV-2 at a community scale. A variety of methods have been used for concentrating, extracting, and detecting the virus, with no clear consensus on the most effective approach. In this note, we report preliminary findings from a study that is tracking SARS-CoV-2 in wastewater in Halifax, Nova Scotia, with a specific focus on the use of four reverse transcriptase quantitative PCR (RT-qPCR) assays for detecting the virus in wastewater. We were able to detect the virus in wastewater samples during the initial rise of cases in the Halifax region in early November 2020. Levels of the targeted SARS-CoV-2 gene fragments increased and fell in response to reported cases of COVID-19. The CDC N1 and E RT-qPCR assays demonstrated greater relative sensitivity than the CDC N2 and N3 assays for detection of SARS-CoV-2 in raw sewage samples. - OPEN ACCESSPost-transcriptional regulators such as microRNAs are emerging as conserved regulators of innate antiviral immunity in vertebrates, yet their roles in amphibian antiviral responses remain uncharacterized. We profiled changes in microRNA expressions in the Xenopus laevis skin epithelial-like cell line Xela DS2 in response to poly(I:C)—an analogue of viral double-stranded RNA and inducer of type I interferons—or frog virus 3 (FV3), an immunoevasive virus associated with amphibian mortality events. Small RNA libraries generated from untreated, poly(I:C)-treated, and FV3-infected cells were sequenced. We detected 136 known X. laevis microRNAs and discovered 133 novel X. laevis microRNAs. Sixty-five microRNAs were differentially expressed in response to poly(I:C), many of which were predicted to target regulators of antiviral pathways such as cGAS-STING, RIG-I/MDA-5, TLR signaling, and type I interferon signaling, as well as products of these pathways (NF-ĸB-induced and interferon-stimulated genes). In contrast, only 49 microRNAs were altered by FV3 infection, fewer of which were predicted to interact with antiviral pathways. Interestingly, poly(I:C) treatment or FV3 infection downregulated transcripts encoding factors of the host microRNA biogenesis pathway. Our study is the first to suggest that host microRNAs regulate innate antiviral immunity in frogs and sheds light on microRNA-mediated mechanisms of immunoevasion by FV3.
- OPEN ACCESS
- Arthur L. Bass,
- Andrew W. Bateman,
- Brendan M. Connors,
- Benjamin A. Staton,
- Eric B. Rondeau,
- Gideon J. Mordecai,
- Amy K. Teffer,
- Karia H. Kaukinen,
- Shaorong Li,
- Amy M. Tabata,
- David A. Patterson,
- Scott G. Hinch, and
- Kristina M. Miller
Recent decades have seen an increased appreciation for the role infectious diseases can play in mass mortality events across a diversity of marine taxa. At the same time many Pacific salmon populations have declined in abundance as a result of reduced marine survival. However, few studies have explicitly considered the potential role pathogens could play in these declines. Using a multi-year dataset spanning 59 pathogen taxa in Chinook and Coho salmon sampled along the British Columbia coast, we carried out an exploratory analysis to quantify evidence for associations between pathogen prevalence and cohort survival and between pathogen load and body condition. While a variety of pathogens had moderate to strong negative correlations with body condition or survival for one host species in one season, we found that Tenacibaculum maritimum and Piscine orthoreovirus had consistently negative associations with body condition in both host species and seasons and were negatively associated with survival for Chinook salmon collected in the fall and winter. Our analyses, which offer the most comprehensive examination of associations between pathogen prevalence and Pacific salmon survival to date, suggest that pathogens in Pacific salmon warrant further attention, especially those whose distribution and abundance may be influenced by anthropogenic stressors. - OPEN ACCESSCyanobacterial blooms and their toxigenic potential threaten freshwater resources worldwide. In Atlantic Canada, despite an increase of cyanobacterial blooms in the last decade, little is known about the toxigenic potential and the taxonomic affiliation of bloom-forming cyanobacteria. In this study, we employed polymerase chain reaction (PCR) and metagenomic approaches to assess the potential for cyanotoxin and other bioactive metabolite production in Harvey Lake (oligotrophic) and Washademoak Lake (mesotrophic) in New Brunswick, Canada, during summer and early fall months. The PCR survey detected the potential for microcystin (hepatotoxin) and anatoxin-a (neurotoxin) production in both lakes, despite a cyanobacterial bloom only being visible in Washademoak. Genus-specific PCR associated microcystin production potential with the presence of Microcystis in both lakes. The metagenomic strategy provided insight into temporal variations in the microbial communities of both lakes. It also permitted the recovery of a near-complete Microcystis aeruginosa genome with the genetic complement to produce microcystin and other bioactive metabolites such as piricyclamide, micropeptin/cyanopeptolin, and aeruginosin. Our approaches demonstrate the potential for production of a diverse complement of bioactive compounds and establish important baseline data for future studies of understudied lakes, which are frequently affected by cyanobacterial blooms.
- OPEN ACCESS
SARS-CoV-2 detection from the built environment and wastewater and its use for hospital surveillance
- Aaron Hinz,
- Lydia Xing,
- Evgueni Doukhanine,
- Laura A. Hug,
- Rees Kassen,
- Banu Ormeci,
- Richard J. Kibbee,
- Alex Wong,
- Derek MacFadden, and
- Caroline Nott
Patients hospitalized with SARS-CoV-2 infections are major contributors to morbidity and mortality in health care settings. Our understanding of the distribution of this virus in the built health care environment and wastewater, and relationship to disease burden, is limited. We performed a prospective multi-center study of environmental sampling of SARS-CoV-2 from hospital surfaces and wastewater and evaluated their relationships with regional and hospital COVID-19 burden. We validated a qPCR-based approach to surface sampling and collected swab samples weekly from different locations and surfaces across two tertiary care hospital campuses for a 10-week period during the pandemic, along with wastewater samples. Over the 10-week period, 963 swab samples were collected and analyzed. We found 61 (6%) swabs positive for SARS-CoV-2, with the majority of these (n = 51) originating from floor samples. Wards that actively managed patients with COVID-19 had the highest frequency of positive samples. Detection frequency in built environment swabs was significantly associated with active cases in the hospital throughout the study. Wastewater viral signal changes appeared to predate change in case burden. Our results indicate that environment sampling for SARS-CoV-2, in particular from floors, may offer a unique and resolved approach to surveillance of COVID-19. - OPEN ACCESSCryptococcus neoformans is a globally important fungal pathogen, primarily inflicting disease on immunocompromised individuals. The widespread use of antifungal agents in medicine and agriculture supports the development of antifungal resistance through evolution, and the emergence of new strains with intrinsic resistance drives the need for new therapeutics. For C. neoformans, the production of virulence factors, including extracellular peptidases (e.g., CnMpr-1 and May1) with mechanistic roles in tissue invasion and fungal survival, constitute approximately 2% of the fungal proteome and cover five classes of enzymes. Given their role in fungal virulence, peptidases represent promising targets for anti-virulence discovery in the development of new approaches against C. neoformans. Additionally, intracellular peptidases, which are involved in resistance mechanisms against current treatment options (e.g., azole drugs), as well as capsule biosynthesis and elaboration of virulence factors, present additional opportunities to combat the pathogen. In this review, we highlight key cryptococcal peptidases with defined or predicted roles in fungal virulence and assess sequence alignments against their human homologs. With this information, we define the feasibility of the select peptidases as “druggable” targets for inhibition, representing prospective therapeutic options against the deadly fungus.
- OPEN ACCESSCoastal salt marshes provide many ecosystem services; however, little is known of the biology of decomposer taxa in these systems. This study employed aboveground and belowground litterbags to characterize the fungal and mite communities associated with the dominant salt marsh grass, Sporobolus pumilus, in the Minas Basin, Nova Scotia. Decomposition rates of aboveground and belowground tissues and environmental variables were quantified to contextualize temporal patterns in community composition. Aboveground litterbag mass loss peaked in July and decreased consistently over succeeding months, which positively correlated with fungal richness. Fungal and mite richness displayed inverse relationships over time, with mites gradually increasing in diversity before peaking in November, suggesting the presence of a complex detrital network where mites and fungi respond to different and possibly unrelated environmental cues. This study offers a first look at temporal community dynamics of two neglected groups of decomposers associated with S. pumilus in Canada.
- OPEN ACCESS
- Isadora Louise Alves da Costa Ribeiro Quintans,
- Juliana Alves da Costa Ribeiro Souza, and
- Michael K Deyholos
Fusarium oxysporum f. sp. lini and Septoria linicola are causes of fusarium wilt and pasmo in flax (Linum usitatissimum). Members of a third fungal genus, Alternaria spp., have also been found in fiber and linseed varieties of flax, and are a source of post-harvest spoilage and mycotoxins in a wide range of crops. We performed a microdilution assay and calculated the median effective concentration (EC50) to compare the potency of cyclolinopeptides (CLPs), two polyamines (spermidine and spermine), and the fungicide carbendazimin in the control of three fungi that have potential pathogenic activity (F. oxysporum, S. linicola, and Alternaria spp), of which the first two are particulary significant causes of disease in flax. For carbendazim, all EC50 values were <0.6 μg/mL. The observed EC50 ranged from 111 to 340 μg/mL for a mixture of six unique CLPs, 109 to 778 μg/mL for spermine, and 21 to 272 μg/mL for spermidine. Spermidine was most effective against Alternaria sp., with an EC50 of 21 μg/mL. The results presented here showed that polyamines and CLPs possess limited antifungal activities against several fungi, with spermidines the most effective naturally occurring compound tested. Our findings do not support the hypothesis that CLPs act as potent antifungals against the three species of pathogens tested.