AMR - One Health Consortium Publications

Myles Leslie, Raad Fadaak, Brendan Cord Lethebe and Jessie Hart Szostakiwskyj

In Canada, the vast majority of antibiotics are prescribed outside of hospitals by family doctors and other members of primary care teams. These community-written antibiotic prescriptions make up 90% of the total volume. Newly released research from Alberta asks how appropriate these prescriptions are. The question is worth asking because inappropriate use of antibiotics contributes to the rise of anti-microbial resistance which occurs when germs adapt, and become immune, to antibiotics. Click here to read the abstract.

Sakib Rahman and Aidan Hollis

This paper estimates the effect of antibiotic usage in humans and food-producing animals on the prevalence of resistance in zoonotic bacteria in both humans and animals. Using comprehensive longitudinal data from annual surveillance reports on resistance and usage in Europe, we find that antibiotic usage in food-producing animals and antibiotic usage in humans are independently and causally related to the prevalence of resistance in both humans and animals.

Christine M. Neustaedter, Kelsey Robertson, Dana Tschritter, Richard J. Reid-Smith, Melissa C. MacKinnon, Colleen P. Murphy, Brennan Chapman, Norman F. Neumann and Simon J. G. Otto

Human infection with antimicrobial-resistant Campylobacter species is an important public health concern due to the potentially increased severity of illness and risk of death. Our objective was to synthesise the knowledge of factors associated with human infections with antimicrobial-resistant strains of Campylobacter. 

Lisa Gamsjäger, Karina M Cirone, Steffany Schluessel, Mackenzie Campsall, Aydin Herik, Priyoshi Lahiri, Daniel Young, Antoine Dufour, Panagiotis Sapountzis, Saria Otani, Diego E Gomez, M Claire Windeyer, Eduardo R Cobo

Calves are highly susceptible to gastrointestinal infection with Cryptosporidium parvum (C. parvum), which can result in watery diarrhea and eventually death or impaired development. With little to no effective therapeutics, understanding the host's microbiota and pathogen interaction at the mucosal immune system has been critical to identify and test novel control strategies. 

Brandon F. Malone, Jason K. Perry, Paul Dominic B. Olinares, Hery W. Lee, James Chen, Todd C. Appleby, Joy Y. Feng, John P. Bilello, Honkit Ng, Johanna Sotiris, Mark Ebrahim, Eugene Y. D. Chua, Joshua H. Mendez, Ed T. Eng, Robert Landick, Matthias Götte, Brian T. Chait, Elizabeth A. Campbell & Seth A. Darst 

This publication outlines the Cryo-EM structure of the SARS-CoV-2 Polymerase with bound remdesivir. The data explains why remdesivir binds so well to this enzyme and supports the development of oral versions of the drug. 

Cristina C.Fodor, RobertMcCorkell, GregMuench, Eduardo R.Cobo

Post-weaning diarrheic colitis, often caused by enteropathogens, are severe and potentially lethal diseases in young pigs. Conventional treatment with antibiotics is problematic due to increasing prevalence of multi-drug resistant bacteria. Few alternative treatments exist, so development of antibiotic-free therapies is urgently needed for livestock. Cathelicidin peptides, produced by epithelial cells and neutrophils, are microbicidal compounds capable of modulating innate immune and inflammatory responses. However, the effects of exogenous cathelicidin on gut homeostasis is poorly understood in pigs. We administered the murine cathelicidin CRAMP systemically to healthy pigs, to establish the peptide’s safety and assess its ability to modulate colonic mucosal defenses. A single intraperitoneal injection of CRAMP was well tolerated up to two weeks and pigs remained clinically healthy. CRAMP caused some alteration of mucus glycosylation patterns in the colon by increasing sialylated mucins (P < 0.05) and decreased neutrophil influx close to the epithelium (P < 0.001). This study supports further investigation of CRAMP as an immunomodulatory treatment for infectious colitis in pigs.

Courtney MacDonald, Anna Bradford, Julia MacGregor, Kristin Flemons, Brian Traynor & John M. Conly 

Antimicrobial resistance (AMR) is widely recognized as one of the greatest threats to public health in the 21^st century. Microbial pathogens including bacteria, viruses, parasites, and fungi are rapidly evolving to become resistant to antimicrobial drugs. Analysis from 2016 reported that at least 700,000 people die every year due to drug-resistant infections; if no action is taken, this number is expected to jump to 10 million human lives per year by 2050 (https://amr-review.org/). Proven methods to help slow the transmission of antimicrobial resistance, such as infection prevention and control practices, and stewardship against misuse and overuse of antimicrobials, are often not effectively implemented due to economic considerations, system inefficiencies, or human behaviour complexities.

In response, our team is developing an online and interactive knowledge translation tool intended to accurately represent complex systems and effectively identify intervention opportunities. Using qualitative research methods, we are mapping out the sociotechnical system of the Canadian beef cattle industry from a One Health perspective. We are engaging with system stakeholders to ensure accuracy and completeness of our information, and consulting potential users to identify the most effective functions and interface characteristics of the tool. We believe that making important system information accessible is crucial to inform opportunities for new products, services and technologies, spark research and business collaborations, prompt consumer awareness and action, and inform policy. Our aim is to create a model that can be emulated to create similar tools in other fields to identify opportunities to help slow the transmission of AMR.

Ruwandi M. Kariyawasam, Danielle A. Julien, Dana C. Jelinski, Samantha L. Larose, Elissa Rennert-May, John M. Conly, Tanis C. Dingle, Justin Z. Chen, Gregory J. Tyrrell, Paul E. Ronksley & Herman W. Barkema

Antimicrobial resistance (AMR) is widely recognized as one of the greatest threats to public health in the 21^st century. Microbial pathogens including bacteria, viruses, parasites, and fungi are rapidly evolving to become resistant to antimicrobial drugs. Analysis from 2016 reported that at least 700,000 people die every year due to drug-resistant infections; if no action is taken, this number is expected to jump to 10 million human lives per year by 2050 (https://amr-review.org/). Proven methods to help slow the transmission of antimicrobial resistance, such as infection prevention and control practices, and stewardship against misuse and overuse of antimicrobials, are often not effectively implemented due to economic considerations, system inefficiencies, or human behaviour complexities.

Etienne J. de Jongh, Sherilee L. Harper, Shelby S. Yamamoto, Carlee J. Wright, Craig W. Wilkinson, Soumyaditya Ghosh, Simon J. G. Otto 

Anthropogenic climate change and increasing antimicrobial resistance (AMR) together threaten the last 50 years of public health gains. Honey bees are a model One Health organism to investigate interactions between climate change and AMR. The objective of this scoping review was to examine the range, extent, and nature of published literature on the relationship between AMR and honey bees in the context of climate change and environmental pollutants. The review followed systematic search methods and reporting guidelines. A protocol was developed a priori in consultation with a research librarian. Resulting Boolean search strings were used to search Embase® via Ovid®, MEDLINE®, Scopus®, AGRICOLA™ and Web of Science™ databases. Two independent reviewers conducted two-stage screening on retrieved articles. To be included, the article had to examine honey bees, AMR, and either climate change or environmental pollution. Data, in accordance with Joanna Briggs Institute guidelines, were extracted from relevant articles and descriptively synthesized in tables, figures, and narrative form. A total of 22 articles met the inclusion criteria, with half of all articles being published in the last five years (n = 11/22). These articles predominantly investigated hive immunocompetence and multi-drug resistance transporter downregulation (n = 11/22), susceptibility to pests (n = 16/22), especially American foulbrood (n = 9/22), and hive product augmentation (n = 3/22). This review identified key themes and gaps in the literature, including the need for future interdisciplinary research to explore the link between AMR and environmental change evidence streams in honey bees. We identified three potential linkages between pollutive and climatic factors and risk of AMR. These interconnections reaffirm the necessity of a One Health framework to tackle global threats and investigate complex issues that extend beyond honey bee research into the public health sector. It is integral that we view these “wicked” problems through an interdisciplinary lens to explore long-term strategies for change.

Kayley D. McCubbin, Herman W. Barkema, Amreen Babujee, Jocelyn Forseille, Kathy Naum, Phil Buote, Darrell Dalton, Sylvia L. Checkley, Keith Lehman, Tricia Morris, Karen Smilski, Wendy L. Wilkins, R. Michele Anholt, Samantha Larose, Lynora M. Saxinger, Dean Blue, Simon J.G. Otto

Source: Canadian Veterinary Journal, VOL. 63, NO. 2, page 198

Access to this publication is restricted to members only. 

Simon J. G. Otto, Margaret Haworth-Brockman, Misha Miazga-Rodriguez, Aleksandra Wierzbowski & Lynora M. Saxinger 

Objective: Integrated surveillance of antimicrobial resistance (AMR) and antimicrobial use (AMU) across One Health sectors is critically important for effective, evidence-based policy, stewardship, and control of AMR. Our objective was to evaluate progress towards achieving comprehensive, integrated AMR/AMU surveillance in Canada.

Materials and methods: Based on an environmental scan, interviews of subject matter experts, and reports from the 2014 National Collaborating Centre for Infectious Diseases and the 2016 Canadian Council of Chief Veterinary Officers, we identified 8 core surveillance requirements and their specific components; the latter were assessed using a 2-way classification matrix, with 7 common elements ranked according to development stage.

Results: Components that mapped to requirements of a comprehensive, fully integrated AMR/AMU surveillance system were mostly in the lowest stages of development (Exploration or Program Adoption). However, both the establishment of the Canadian AMR Surveillance System integrated reporting and expansion of existing components under the Canadian Nosocomial Infection Surveillance Program and the Canadian Integrated Program for AMR Surveillance are improvements. Regardless, obvious gaps in Canadian AMR/AMU surveillance prevent this from being a comprehensive and integrated One Health program.

Conclusion: Action is needed in 3 crucial areas: i) development of a complete, integrated AMR/AMU surveillance program, based on current success; ii) changes in Federal/Provincial/Territorial policies to require standardized AMR/AMU reporting; and iii) more resources for AMR/AMU surveillance (dedicated persons, funding, and enabling structures and policy). There is an urgent need for prioritization by Federal/Provincial/Territorial governments to address governance, leadership, and funding to create surveillance systems that inform stewardship and policy.

Xuechun Bai & Graham S. Plastow

Disease resilience, defined as an animal’s ability to maintain productive performance in the face of infection, provides opportunities to manage the polymicrobial challenge common in pig production. Disease resilience can deliver a number of benefits, including more sustainable production as well as improved animal health and the potential for reduced antimicrobial use. However, little progress has been made to date in the application of disease resilience in breeding programs due to a number of factors, including (1) confusion around definitions of disease resilience and its component traits disease resistance and tolerance, and (2) the difficulty in characterizing such a complex trait consisting of multiple biological functions and dynamic elements of rates of response and recovery from infection. Accordingly,
this review refines the definitions of disease resistance, tolerance, and resilience based on previous studies to help improve the understanding and application of these breeding goals and traits under different scenarios. We also describe and summarize results from a “natural disease challenge model” designed to provide inputs for selection of disease resilience. The next steps for managing polymicrobial challenges faced by the pig industry will include the development of large-scale multi-omics data, new phenotyping technologies, and mathematical and statistical methods adapted to these data. Genome editing to produce pigs resistant to major diseases may complement selection for disease resilience along with continued efforts in the more traditional areas of biosecurity, vaccination and treatment. Altogether genomic approaches provide exciting opportunities for the pig industry to overcome the challenges provided by hard-to-manage diseases as well as new environmental challenges associated with climate
change.

Justin Ancheta, Raad Fadaak, R. Michele Anholt, Danielle Julien, Herman W. Barkema, Myles Leslie

Zoonotic diseases have become a major worldwide challenge; with COVID-19 being the latest and most dramatic example of an animal-derived virus affecting humans. With COVID-19 and previous zoonotic disease epidemics, the concept of One Health has gained prominence (1). Based upon several hundred years of thinking and social development, One Health has developed a holistic, systems approach to address complex problems at the intersection of humans, animals, and the environment. This paper summarizes evolving and competing ideas underlying contemporary One Health concepts and practices. In the 17th and 18th centuries, important figures in veterinary medicine aligned aspects of human and animal medicine, thereby initiating comparative medicine (2). In 1761, Claude Bourgelat founded the first veterinary college in Lyon, France. This college, focused entirely on horses, made veterinary medicine a distinct discipline. Paradoxically, separation of veterinary medicine from human medicine benefitted One Health, as it initiated an advantageous and reciprocal flow of ideas and perspectives between human and animal medicine. As veterinary researchers moved away from framing disease in exclusively human terms, a new view of health emerged, leading to investigations of herd animal health, with findings informing human health. In addition, Bourgelat introduced comparative pathology (3)

Margaret Haworth-Brockman, Lynora M. Saxinger, Misha Miazga-Rodriguez, Aleksandra Wierzbowski, and Simon J. G. Otto

We describe the development, application and utility of our novel, One Health Evaluation of Antimicrobial Use and Resistance Surveillance (OHE-AMURS) tool that we created to evaluate progress toward integrated, One Health surveillance of antimicrobial resistance (AMR) and antimicrobial use (AMU) as a complex system in Canada. We conducted a qualitative inquiry into the current state of policy and programs for integrated AMR/AMU surveillance using explicit and tacit knowledge. To assess the “messy” state of public health surveillance program development, we synthesized recommendations from previous reports by the National Collaborating Centre for Infectious Diseases and the Canadian Council of Chief Veterinary Officers; conducted an environmental scan to find all federal, provincial, and territorial AMR/AMU surveillance programs in Canada; and conducted semi-structured interviews with Canadian subject matter experts. To integrate evidence from these different sources we adapted two published tools to create a new evaluation matrix, deriving 36 components of the ideal integrated AMR/AMU surveillance system. Our two-way matrix tool allowed us to examine seven common, foundational elements of sustainable programs for each component, and assign a stage of development/sustainability ranking for each component according to the matrix definitions. Our adaptable novel tool allowed for granular and repeatable assessment of the many components of a complex surveillance system. The assessment proved robust and exacting to ensure transparency in our methods and results. The matrix allows flexible assignment of program components based on program principles, and stages can be adapted to evaluate any aspect of an AMR/AMU surveillance or other multi-faceted, multi-jurisdictional system. Future refinement should include an assessment of the scope of surveillance components.

Lindsay A. Rogers, Kayla Strong, Susan C. Cork, Tim A. McAllister, Karen Liljebjelke, Rahat Zaheer and Sylvia L. Checkley

Enterococcus spp. have arisen as important nosocomial pathogens and are ubiquitous in the gastrointestinal tracts of animals and the environment. They carry many intrinsic and acquired antimicrobial resistance genes. Because of this, surveillance of Enterococcus spp. has become important with whole genome sequencing emerging as the preferred method for the characterization of enterococci. A scoping review was designed to determine how the use of whole genome sequencing in the surveillance of Enterococcus spp. adds to our knowledge of antimicrobial resistance in Enterococcus spp. Scoping review design was guided by the PRISMA extension and checklist and JBI Reviewer's Guide for scoping reviews. A total of 72 articles were included in the review. Of the 72 articles included, 48.6% did not state an association with a surveillance program and 87.5% of articles identified Enterococcus faecium. The majority of articles included isolates from human clinical or screening samples. Significant findings from the articles included novel sequence types, the increasing prevalence of vancomycin-resistant enterococci in hospitals, and the importance of surveillance or screening for enterococci. The ability of enterococci to adapt and persist within a wide range of environments was also a key finding. These studies emphasize the importance of ongoing surveillance of enterococci from a One Health perspective. More studies are needed to compare the whole genome sequences of human enterococcal isolates to those from food animals, food products, the environment, and companion animals.

AMR - One Health Consortium, Content Expert(s): Aidan Hollis, PhD

Given the urgent need for new antibiotics, Canada should explore supporting novel antibiotics through market entry rewards, in line with new policies in the UK and Sweden, and as proposed in the US. This would also motivate patentees to seek timely approval of antibiotics in Canada.

Simon Otto, Misha Miazga-Rodriguez Lynora Saxinger

Antimicrobial resistance (AMR) is a recognized global threat to health security. Integrated One Health surveillance of AMR and antimicrobial use (AMU) must underpin efforts to protect human, animal, and crop health. In 2014, the National Collaborating Centre for Infectious Diseases (NCCID) published a report commissioned to assess the status of AMR/AMU surveillance in Canada including the authors’ recommendations to address gaps in Canada. In 2016, the Canadian Council of Chief Veterinary Officers (CCVO) released a report evaluating options to strengthen AMU surveillance in animals in Canada that mapped within the AMU surveillance recommendations of the NCCID report.

Jacob A. Narbonne, Brian R. Radke, Derek Price, Patrick C. Hanington, Amreen Babujee, and Simon J. G. Otto

Quantification and tracking of antimicrobial use (AMU) are key factors for the development of responsible antimicrobial stewardship programs and comparison between countries. Global finfish aquaculture growth and increased AMU creates the potential for exchange of antimicrobial resistance between aquatic and terrestrial environments, making AMU surveillance imperative for this industry. The objective of this review is to collate current literature on AMU surveillance indicators and their application to commercial finfish aquaculture production. A systematic search strategy was applied to five databases: Medline, Embase, Agricola, CAB abstracts, and Biosis. To be included, studies must report on at least one AMU surveillance indicator for use in animals. There is no single, standardized indicator suitable to report finfish aquaculture AMU. The type and availability of finfish aquaculture data presents unique considerations for AMU reporting. Ultimately, the indicator used should be fit-for-purpose to satisfy the objective of the surveillance program, motivation for comparison and provide useful information to the industry stakeholders. Finfish aquaculture total annual slaughter weight allows estimation of biomass for the population correction unit (PCU) to report annual total mg of active antimicrobial ingredient per PCU. These data are commonly reported by finfish aquaculture-producing countries, allowing for international comparisons. However, this precludes the ability to compare to terrestrial livestock where the PCU is based on animal numbers and an average treatment weight, which are not available for finfish aquaculture. The mg per adjusted PCU indicator provides an interesting alternative that incorporates the length of the marine grow-out phase for finfish, but is subject to the same limitations. The number of defined daily doses animal per animal-days-at-risk is useful but also limited by a lack of a defined average treatment weight. The concept of average treatment weight remains challenging for the industry as it does not accurately reflect the timing of actual AMU to fish in the system. The term “average biomass” is more reflective of the intent of AMU surveillance indicators. Defining an average treatment weight, or average biomass, will require industry engagement, which is crucial if AMU reporting is to be deemed credible and provide value back to the finfish aquaculture industry.

Janelle Jiminez, Edouard Timsit, Karin Orsel, Frank van der Meer, Le Luo Guan and Graham Plastow

Bovine respiratory disease (BRD) is one of the main factors leading to morbidity and mortality in feedlot operations in North America. A complex of viral and bacterial pathogens can individually or collectively establish BRD in cattle, and to date, most disease characterization studies using transcriptomic techniques examine bronchoalveolar and transtracheal fluids, lymph node, and lung tissue as well as nasopharyngeal swabs, with limited studies investigating the whole-blood transcriptome. Here, we aimed to identify differentially expressed (DE) genes involved in the host immune response to BRD using whole blood and RNA sequencing. Samples were collected from heifers (average arrival weight = 215.0  5.3 kg) with (n = 25) and without (n = 18) BRD at a commercial feedlot in Western Canada. RNAseq analysis showed a distinct whole-blood transcriptome profile between BRD and non-BRD heifers. Further examination of the DE genes revealed that those involved in the host inflammatory response and infectious disease pathways were enriched in the BRD animals, while gene networks associated with metabolism and cell growth and maintenance were downregulated. Overall, the transcriptome profile derived from whole blood provided evidence that a distinct antimicrobial peptide-driven host immune response was occurring in the animals with BRD. The blood transcriptome of the BRD animals shows similarities to the transcriptome profiles obtained from lung and bronchial lymph nodes in other studies. This suggests that the blood transcriptome is a potential diagnostic tool for the identification of biomarkers of BRD infection and can be measured in live animals and used to further understand infection and disease in cattle. It may also provide a useful tool to increase the understanding of the genes involved in establishing BRD in beef cattle and be used to investigate potential therapeutic applications.

Sakib Rahman, Olof Lindahl, Chantal M. Morel, Aidan Hollis

We calculate the average sales of new antibiotics during their first 8 years on the market. The discounted net present value is only $240 m in total per antibiotic, well below costs of supplying these products. The reliance on the US for sales is striking: the US market accounts for 84% of sales during the first 8 years. These facts clarify the need for additional revenues, especially from other countries, to support incentives for the development of new antibiotics. Market entry rewards may be of particular value.

Brendan Todd, Egor P. Tchesnokov and Matthias Götte

Baloxavir marboxil (BXM) is an FDA-approved antiviral prodrug for the treatment of influenza A and B infection and post-exposure prophylaxis. The active form, baloxavir acid (BXA), targets the cap-snatching endonuclease (PA) of the influenza virus polymerase complex. The nuclease activity delivers the primer for transcription and previous reports have shown that BXA blocks the nuclease activity with high potency. However, biochemical studies on the mechanism of action are lacking. Structural data have shown that BXA chelates the two divalent metal ions at the active site, like inhibitors of the human immunodeficiency virus type 1 (HIV-1) integrase or ribonuclease (RNase) H. Here we studied the mechanisms underlying the high potency of BXA and how the I38T mutation confers resistance to the drug. Enzyme kinetics with the recombinant heterotrimeric enzyme (FluB-ht) revealed characteristics of a tight binding inhibitor. The apparent inhibitor constant (K_i^app) is 12 nM, while the I38T mutation increased K_i^app by ∼18-fold. Order-of-addition experiments show that a preformed complex of FluB-ht, Mg²⁺ ions and BXA is required to observe inhibition, which is consistent with active site binding. Conversely, a preformed complex of FluB-ht and RNA substrate prevents BXA from accessing the active site. Unlike integrase inhibitors that interact with the DNA substrate, BXA behaves like RNase H inhibitors that compete with the nucleic acid at the active site. The collective data support the conclusion that BXA is a tight binding inhibitor and the I38T mutation nishes these prdimioperties.

Gregory J. Tyrrell, Christopher Bell, Lea Bill, Sumana Fathima

The incidence of invasive group A Streptococcus (iGAS) disease in the general population in Alberta, Canada, has been steadily increasing. To determine whether rates for specific populations such as First Nations are also increasing, we investigated iGAS cases among First Nations persons in Alberta during 2003–2017. We identified cases by isolating GAS from a sterile site and performing emm typing. We collected demographic, social, behavioral, and clinical data for patients. During the study period, 669 cases of iGAS in First Nations persons were reported. Incidence increased from 10.0 cases/100,000 persons in 2003 to 52.2 cases/100,000 persons in 2017. The 2017 rate was 6 times higher for the First Nations population than for non–First Nations populations (8.7 cases/100,000 persons). The 5 most common emm types from First Nations patients were 59, 101, 82, 41, and 11. These data indicate that iGAS is severely affecting the First Nations population in Alberta, Canada.

Carly M. Davis , Jaclyn G. McCutcheon and Jonathan J. Dennis 

Pseudomonas aeruginosa is a pernicious bacterial pathogen that is difficult to treat because of high levels of antibiotic resistance. A promising alternative treatment option for such bacteria is the application of bacteriophages; the correct combination of phages plus antibiotics can produce synergistic inhibitory effects. In this study, we describe morphological changes induced by sub-MIC levels of the antibiotic aztreonam lysine (AzLys) on P. aeruginosa PA01, which may in part explain the observed phage–antibiotic synergy (PAS). One-step growth curves for phage E79 showed increased adsorption rates, decreased infection latency, accelerated time to lysis and a minor reduction in burst size. Phage E79 plus AzLys PAS was also able to significantly reduce P. aeruginosa biofilm growth over 3-fold as compared to phage treatment alone. Sub-inhibitory AzLys-induced filamentation of P. aeruginosa cells resulted in loss of twitching motility and a reduction in swimming motility, likely due to a reduction in the number of polar Type IV pili and flagella, respectively, on the filamented cell surfaces. Phage phiKZ, which uses Type IV pili as a receptor, did not exhibit increased activity with AzLys at lower sub-inhibitory levels, but still produced phage–antibiotic synergistic killing with sub-inhibitory AzLys. A one-step growth curve indicates that phiKZ in the presence of AzLys also exhibits a decreased infection latency and moderately undergoes accelerated time to lysis. In contrast to prior PAS studies demonstrating that phages undergo delayed time to lysis with cell filamentation, these PAS results show that phages undergo accelerated time to lysis, which therefore suggests that PAS is dependent upon multiple factors, including the type of phages and antibiotics used, and the bacterial host being tested.

Diego B. Nobrega, S. Ali Naqvi, Simon Dufour, Rob Deardon, John P. Kastelic, Jeroen De Buck, and Herman W. Barkema 

There is ongoing debate regarding whether critically important antimicrobials (CIA) should be used to treat infections in food-producing animals. In this systematic review, we determined whether CIA and non-CIA have comparable efficacy to treat nonsevere bovine clinical mastitis caused by the most commonly reported bacteria that cause mastitis worldwide. We screened CAB Abstracts, Web of Science, MEDLINE, Scopus, and PubMed for original epidemiological studies that assessed pathogen-specific bacteriological cure rates of antimicrobials used to treat nonsevere clinical mastitis in lactating dairy cows. Network models were fit using risk ratios of bacteriological cure as outcome. A total of 30 studies met inclusion criteria. Comparisons of cure rates demonstrated that CIA and non-CIA had comparable efficacy for treatment of nonsevere clinical mastitis in dairy cattle. Additionally, for cows with nonsevere clinical mastitis caused by Escherichia coli and Klebsiella spp., bacteriological cure rates were comparable for treated versus untreated cows; therefore, there was no evidence to justify treatment of these cases with CIA. Our findings supported that CIA in general are not necessary for treating nonsevere clinical mastitis in dairy cattle, the disease that accounts for the majority of antimicrobial usage in dairy herds worldwide. Furthermore, our findings support initiatives to reduce or eliminate use of CIA in dairy herds.

Jaclyn G. McCutcheon, Andrea Lin, Jonathan J. Dennis

The rapid increase in the number of worldwide human infections caused by the extremely antibiotic resistant bacterial pathogen Stenotrophomonas maltophilia is cause for concern. An alternative treatment solution in the post-antibiotic era is phage therapy, the use of bacteriophages to selectively kill bacterial pathogens. In this study, the novel bacteriophage AXL3 (vB_SmaS-AXL_3) was isolated from soil and characterized. Host range analysis using a panel of 29 clinical S. maltophilia isolates shows successful infection of five isolates and electron microscopy indicates that AXL3 is a member of the Siphoviridae family. Complete genome sequencing and analysis reveals a 47.5 kb genome predicted to encode 65 proteins. Functionality testing suggests AXL3 is a virulent phage and results show that AXL3 uses the type IV pilus, a virulence factor on the cell surface, as its receptor across its host range. This research identifies a novel virulent phage and characterization suggests that AXL3 is a promising phage therapy candidate, with future research examining modification through genetic engineering to broaden its host range.

Myles Leslie, Raad Fadaak, Jan Davies, Johanna Blaak, P G Forest, Lee Green, John Conly

This paper outlines the rapid integration of social scientists into a Canadian province's COVID-19 response. We describe the motivating theory, deployment and initial outcomes of our team of Organisational Sociologist ethnographers, Human Factors experts and Infection Prevention and Control clinicians focused on understanding and improving Alberta's responsiveness to the pandemic. Specifically, that interdisciplinary team is working alongside acute and primary care personnel, as well as public health leaders to deliver 'situated interventions' that flow from studying communications, interpretations and implementations across responding organisations. Acting in real time, the team is providing critical insights on policy communication and implementation to targeted members of the health system. Using our rapid and ongoing deployment as a case study of social science techniques applied to a pandemic, we describe how other health systems might leverage social science to improve their preparations and communications.

Author: AMR - One Health Consortium, Content Expert(s): Matthias Götte, PhD; John Conly, MD

During the COVID-19 pandemic, treating hospitalized patients with severe diseaseh as been a primary concern of healthcare providers. Shortening the course of the illness, reducing length of hospital stay, and reducing mortality are crucial treatment goals. Successful treatment would alleviate patient suffering, decrease the burden on healthcare system costs, and increase the availability of resources for other acute care patients. Remdesivir is an investigational antiviral drug that was shown to address this issue. However, neither remdesivir nor any other antiviral agent is currently approved for the treatment of COVID-19 in Canada.

Hui-Zeng Sun; Vythegi Srithayakumar; Janelle Jiminez; Weiwu Jin; Afshin Hosseini; Mikolaj Raszek; Karin Orsel; Le Luo Guan; Graham Plastow

Bovine respiratory disease (BRD) is the most common disease in beef cattle and leads to considerable economic losses in both beef and dairy cattle. It is important to uncover the molecular mechanisms underlying BRD and to identify biomarkers for early identification of BRD cattle in order to address its impact on production and welfare. In this study, a longitudinal transcriptomic analysis was conducted using blood samples collected from 24 beef cattle at three production stages in the feedlot: 1) arrival (Entry group); 2) when identified as sick (diagnosed as BRD) and separated for treatment (Pulled); 3) prior to marketing (Close-out, representing healthy animals). Expressed genes were significantly different in the same animal among Entry, Pulled and Close-out stages (false discovery rate (FDR) < 0.01 & |Fold Change| > 2). Beef steers at both Entry and Pulled stages presented obvious difference in GO terms (FDR < 0.05) and affected biological functions (FDR < 0.05 & |Z-score| > 2) when compared with animals at Close-out. However, no significant functional difference was observed between Entry and Pulled animals. The interferon signaling pathway showed the most significant difference between animals at Entry/Pulled and Close-out stages (P < .001 & |Z-score| > 2), suggesting the animals initiated antiviral responses at an early stage of infection. Six key genes including IFI6, IFIT3, ISG15, MX1, and OAS2 were identified as biomarkers to predict and recognize sick cattle at Entry. A gene module with 169 co-expressed genes obtained from WGCNA analysis was most positively correlated (R = 0.59, P = 6E-08) with sickness, which was regulated by 11 transcription factors. Our findings provide an initial understanding of the BRD infection process in the field and suggests a subset of novel marker genes for identifying BRD in cattle at an early stage of infection.

Danielle L. Peters, Jaclyn G. McCutcheon, and Jonathan J. Dennis^*

A novel Siphoviridae phage specific to the bacterial species Stenotrophomonas maltophilia was isolated from a pristine soil sample and characterized as a second member of the newly established Delepquintavirus genus. Phage DLP3 possesses one of the broadest host ranges of any S. maltophilia phage yet characterized, infecting 22 of 29 S. maltophilia strains. DLP3 has a genome size of 96,852 bp and a G+C content of 58.4%, which is significantly lower than S. maltophilia host strain D1571 (G+C content of 66.9%). The DLP3 genome encodes 153 coding domain sequences covering 95% of the genome, including five tRNA genes with different specificities. The DLP3 lysogen exhibits a growth rate increase during the exponential phase of growth as compared to the wild type strain. DLP3 also encodes a functional erythromycin resistance protein, causing lysogenic conversion of the host D1571 strain. Although a temperate phage, DLP3 demonstrates excellent therapeutic potential because it exhibits a broad host range, infects host cells through the S. maltophilia type IV pilus, and exhibits lytic activity in vivo. Undesirable traits, such as its temperate lifecycle, can be eliminated using genetic techniques to produce a modified phage useful in the treatment of S. maltophilia bacterial infections.

Jinshui Zheng, Stijn Wittouck, Elisa Salvetti, Charles M.A.P. Franz​, Hugh M.B. Harris, Paola Mattarelli, Paul W. O’Toole5​, Bruno Pot, Peter Vandamme, Jens Walter, Koichi Watanabe, Sander Wuyts, Giovanna E. Felis, Michael G. Gänzle, Sarah Lebeer

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus , which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae . The generic term ‘lactobacilli’ will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii , Lactobacillus iners , Lactobacillus crispatus , Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus ) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola ).

Gordon, C., Tchesnokov, E., Woolner, E., Perry, J., Feng, J., Porter, D., and Gotte, M. 

Effective treatments for coronavirus disease 2019 (COVID-19) are urgently needed to control this current pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Replication of SARS-CoV-2 depends on the viral RNA-dependent RNA polymerase (RdRp), which is the likely target of the investigational nucleotide analogue remdesivir (RDV). RDV shows broad-spectrum antiviral activity against RNA viruses, and previous studies with RdRps from Ebola virus (EBOV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have revealed that delayed chain-termination is RDV’s plausible mechanism of action. Here, we expressed and purified active SARS-CoV-2 RdRp composed of the non-structural proteins nsp8 and nsp12. Enzyme kinetics indicated that this RdRp efficiently incorporates the active triphosphate form of RDV (RDV-TP) into RNA. Incorporation of RDV-TP at position i caused termination of RNA synthesis at position i+3. We obtained almost identical results with SARS-CoV, MERS-CoV, and SARS-CoV-2 RdRps. A unique property of RDV-TP is its high selectivity over incorporation of its natural nucleotide counterpart ATP. In this regard, the triphosphate forms of 2’-C–methylated compounds, including sofosbuvir, approved for the management of hepatitis C virus infection, and the broad-acting antivirals favipiravir and ribavirin, exhibited significant deficits. Furthermore, we provide evidence for the target specificity of RDV, as RDV-TP was less efficiently incorporated by the distantly related Lassa virus RdRp, and termination of RNA synthesis was not observed. These results collectively provide a unifying, refined mechanism of RDV-mediated RNA synthesis inhibition in coronaviruses and define this nucleotide analogue as a direct-acting antiviral (DAA).

Simon J.G. Otto, Paul N. Levett, Richard J. Reid-Smith, David L. Pearl, Dawn Daku, Evelyn Nagle, Greg B. Horsman, and Scott A. McEwen

To describe a historical baseline of antimicrobial resistance (AMR) profiles for human clinical Campylobacter species isolates obtained by laboratory surveillance in the province of Saskatchewan from 1999 to 2006; to determine if there were differences in resistance between Campylobacter jejuni and Campylobacter coli; and to determine if there were changes in the annual resistance levels in the two species. One thousand three hundred seventy-eight Campylobacter isolates were subjected to antimicrobial susceptibility testing using the E-test method. Annual resistance levels in C. jejuni and C. coli were compared using logistic regression models. One thousand two hundred (87.1%) isolates were C. jejuni and 129 (9.4%) were C. coli. Resistance in C. jejuni isolates included ciprofloxacin (CIP: 9.4%), erythromycin (ERY: 0.5%), and tetracycline (33.3%). CIP resistance in C. jejuni was higher in 1999 (15.5%, odds ratio [OR] = 3.96, p = 0.01), 2000 (12.7%, OR = 3.10, p = 0.01), 2005 (10.2%, OR = 2.47, p = 0.05), and 2006 (13.0%, OR = 3.22, p = 0.01) compared with 2004 (4.4%). C. coli had significantly higher CIP resistance (15.5%, OR = 1.78, p = 0.03), ERY resistance (13.2%, OR = 60.12, p < 0.01), multidrug resistance (2.3%, OR = 36.29, p < 0.01), and CIP-ERY resistance (3.1%, OR = 50.23, p < 0.01) compared with C. jejuni. This represents the first and most current report of AMR of the collective human Campylobacter isolates from a province in Canada and provides a baseline against which current and future resistance patterns can be compared. Fluoroquinolone resistance in C. jejuni isolates fluctuated from 1999 to 2006, including an increased prevalence in 2005–2006, while macrolide/lincosamide resistance remained very low. Human clinical C. jejuni isolates from Saskatchewan demonstrated resistance to multiple antimicrobials but had significantly less fluoroquinolone and macrolide resistance than C. coli isolates.

Xuechun Bai, Austin M. Putz, Zhiquan Wang, Frédéric Fortin, John C. S. Harding, Michael K. Dyck, Jack C. M. Dekkers, Catherine J. Field, Graham S. Plastow, and PigGen Canada

Disease resilience is a valuable trait to help manage infectious diseases in livestock. It is anticipated that improved disease resilience will sustainably increase production efficiency, as resilient animals maintain their performance in the face of infection. The objective of this study was to identify phenotypes related to disease resilience using complete blood count (CBC) data from a wean-to-finish natural disease challenge model, established to mimic the disease pressure caused by many common pathogens at the commercial level of pig production. In total, 2433 F1 crossbred (Landrace × Yorkshire) barrows that went through the natural disease challenge model were classified into four groups (resilient, average, susceptible, and dead) based on their divergent responses in terms of growth and individual treatment. Three sets of blood samples for CBC analysis were drawn at 2-weeks before, and at 2- and 6-weeks after the challenge: Blood 1, Blood 3, and Blood 4 respectively. CBC of Blood 1 taken from healthy pigs before challenge did not show differences between groups. However, resilient animals were found to be primed to initiate a faster adaptive immune response and recover earlier following infection, with greater increases of lymphocyte concentration from Blood 1 to Blood 3 and for hemoglobin concentration and hematocrit from Blood 3 to Blood 4, but a lower neutrophil concentration from Blood 3 to Blood 4 than in susceptible and dead animals (FDR < 0.05). The CBC traits in response to the challenge were found to be heritable and genetically correlated with growth and treatment, which may indicate the potential for developing CBC under disease or commercial conditions as a phenotype in commercial systems as part of developing predictions for disease resilience.

Rahat Zaheer, Shaun R. Cook, Ruth Barbieri, Noriko Goji, Andrew Cameron, Aaron Petkau, Rodrigo O rtega Polo, Lisa Tymensen, Courtney Stamm, Jiming Song, Sherry Hannon, Tineke Jones, Deirdre Church, Calvin W. Booker, Kingsley Amoako, Gary Van Domselaar, Ron R. Read & Tim A. McAllister

For a One-Health investigation of antimicrobial resistance (AMR) in Enterococcus spp., isolates from humans and beef cattle along with abattoirs, manured fields, natural streams, and wastewater from both urban and cattle feedlot sources were collected over two years. Species identification of Enterococcus revealed distinct associations across the continuum. Of the 8430 isolates collected, Enterococcus faecium and Enterococcus faecalis were the main species in urban wastewater (90%) and clinical human isolates (99%); Enterococcus hirae predominated in cattle (92%) and feedlot catch-basins (60%), whereas natural streams harbored environmental Enterococcus spp. Wholegenome sequencing of E. faecalis (n = 366 isolates) and E. faecium (n = 342 isolates), revealed source clustering of isolates, indicative of distinct adaptation to their respective environments. Phenotypic resistance to tetracyclines and macrolides encoded by tet(M) and erm(B) respectively, was prevalent among Enterococcus spp. regardless of source. For E. faecium from cattle, resistance to β-lactams and quinolones was observed among 3% and 8% of isolates respectively, compared to 76% and 70% of human clinical isolates. Clinical vancomycin-resistant E. faecium exhibited high rates of multi-drug resistance, with resistance to all β-lactam, macrolides, and quinolones tested. Differences in the AMR profiles among isolates reflected antimicrobial use practices in each sector of the One-Health continuum.

Chantal M. Morel, Olof Lindahl, Stephan Harbarth, Marlieke E. A. de Kraker, Suzanne Edwards & Aidan Hollis

The scarcity of novel antibiotic compounds in a time of increasing resistance rates has begun to ring alarm bells at the highest echelons of government. Large new financial incentives to accelerate antibiotic research and development, such as market entry rewards (MERs), are being considered. However, there is little focus on how to sustain the efficacy of new, promising antibiotics reaching the market. Currently, inappropriate use of antibiotics is commonplace, which has accelerated resistance development. In an attempt to halt this trend, antibiotic stewardship policies are being implemented in many resource-rich settings. Unfortunately, this has not yet had an impact on the amount of antibiotics being prescribed globally. One important hurdle is misalignment of incentives. While governments and health services are incentivized to promote prudent use of this common good, pharmaceutical companies are incentivized to increase volume of sales to maximize profits. This problem must be addressed or else the major efforts going into developing new antibiotics will be in vain. In this paper we outline an approach to realign the incentives of pharmaceutical companies with wider antibiotic conservation efforts by making a staged bonus a component of an MER for antibiotic developers when resistance to their drug remains low over time. This bonus could address the lack of stewardship focus in any innovation-geared incentive.

A. Sharma, D.R. Pillai, M. Lua, C. Doolan, J. Leal, J. Kim, A. Hollis

Impact of isolation precautions on psychological wellbeing of patients has yet to be fully quantified. To assess the impact of isolation precautions on patients' health-related quality of life and depression or anxiety scales and estimate per day cost of anxiety and depression. Literature pertaining to impact of isolation precautions was searched on EMBASE and PubMed databases and Google Scholar. A two-step independent screening of the articles was performed. Articles that compared isolated and non-isolated patients using different quality of life and psychological burden scales were included. A meta-analysis was conducted using the Hospital Anxiety and Depression Scales (HADS-A and HADS-D). Psychological burden measures from selected literature were presented in a graph as effect sizes. Per day cost of anxiety and depression was estimated using pooled mean difference from meta-analysis. Out of 106 articles, 94 were excluded due to inclusion criteria, leaving 12 for full text review. After review of full text of the articles, seven articles were shortlisted for empirical analysis and four out of these seven for meta-analysis. The pooled mean difference estimates for HADS-A was Math Eq (P=0.15) and that for HADS-D was Math Eq (P=0.09). In the empirical analysis of psychological burden scales, the effect in all studies except one was negative. Results from meta-analysis and empirical analysis of psychological burden implied that isolated patients are worse off in general. The implied estimated per day cost of anxiety and depression in terms of quality-adjusted life years (QALYs) is approximately US$10.

Calvin J. Gordon, Egor P. Tchesnokov, Joy Y. Feng, Danielle P. Porter, and Matthias Götte

Antiviral drugs for managing infections with human coronaviruses are not yet approved, posing a serious challenge to current global efforts aimed at containing the outbreak of severe acute respiratory syndrome–coronavirus 2 (CoV-2). Remdesivir (RDV) is an investigational compound with a broad spectrum of antiviral activities against RNA viruses, including severe acute respiratory syndrome–CoV and Middle East respiratory syndrome (MERS–CoV). RDV is a nucleotide analog inhibitor of RNA-dependent RNA polymerases (RdRps). Here, we co-expressed the MERS–CoV nonstructural proteins nsp5, nsp7, nsp8, and nsp12 (RdRp) in insect cells as a part a polyprotein to study the mechanism of inhibition of MERS–CoV RdRp by RDV. We initially demonstrated that nsp8 and nsp12 form an active complex. The triphosphate form of the inhibitor (RDV-TP) competes with its natural counterpart ATP. Of note, the selectivity value for RDV-TP obtained here with a steady-state approach suggests that it is more efficiently incorporated than ATP and two other nucleotide analogs. Once incorporated at position i, the inhibitor caused RNA synthesis arrest at position i + 3. Hence, the likely mechanism of action is delayed RNA chain termination. The additional three nucleotides may protect the inhibitor from excision by the viral 3′–5′ exonuclease activity. Together, these results help to explain the high potency of RDV against RNA viruses in cell-based assays.

Check out a recent magazine article of a project from Jon Dennis lab, one of the AMR - One Health Co-Investigators

Author: Mark Czarneckljan

Date: January, 2020

Summary

A Canadian scientist once harnessed the power of viruses against bacterial infections. In dire times, a new generation of scientists is fighting to do the same.