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AMR Symposium Poster Presentations

2025 Annual AMR Symposium Poster presentations (alphabetical by author)

Dalia Ali,Chemistry and Biochemistry,Concordia University,Supervisor:Christine DeWolf
"Phytoglycogen nanoparticles: a promising nanocarrier for the inhalation delivery of antibiotics"

󲹰dzܲ, Microbiology and Immunology, University of Montreal, Supervisor:Yves Brun
"Mapping the Morphological Landscape to Uncover Gene Function in Escherichia coli"

Khlood Alsulami,Medicine,51Թ, Supervisor: Alexander Lawandi
"Comparison of Direct Disc and Vitek2 Antimicrobial Susceptibility Testing on Positive Blood Cultures from Healthcare Facilities Across Quebec, 2020-2024"

Khlood Alsulami, Medicine, 51Թ, Supervisor: Alexander Lawandi
"Dynamic changes in Staphylococcus aureus Penicillin Binding Protein isoform profiles during growth and antibiotic exposure"

Antoine Bignet,Microbiology and Biotechnology,INRS,Supervisor: Salim Timo Islam
"Implementation of a drug-discovery pipeline to identify polysaccharide secretion-blocking compound"

AdwaithBini Bose Uday, Anatomy and Cell Biology, 51Թ, Supervisor: Salim Timo Islam
"Structural basis for allosteric regulation of the proteasome core particle"

Ƿ, Biology, 51Թ, Supervisor: Rees Kassen
"Compensatory Mutations and the Evolution of Reduced-costs of Resistance in Pseudomonas aeruginosa."

Farhan Rahman Chowdhury,Biology, Concordia University,Supervisor: Brandon Findlay[Flash Talk #3]
"Recycling Antibiotics: Tripartite Drug Cycling Reverses Antibiotic Resistance"

ܰԳdzܳٳܰ,Biology,Université de Sherbrooke,Supervisor: Jean-Philippe Côté[Flash Talk #6]
"High-throughput tools to probe Salmonella-gut microbiota dynamics"

RayanDjavedani Hadji,Chemistry & Biochemistry, Concordia University, Supervisor: Brandon Findlay
"Harnessing Stress-Induced Biosynthesis for Natural Product Discovery"

Lucas Elliott,Bioengineering, 51Թ, Supervisor: Codruta Ignea and Lisa Munter
"Nucle.io: A rapid point-of-care diagnostic platform for bacterial identification"

ٱ󲹰첹,Microbiology and Immunology,51Թ,Supervisor: Dao Nguyen
"Screening and analysis of antibiotic production by Canadian High Arctic bacteria"

մDZܷɲ󲹳ٴǰ쾱, Chemistry and Biochemistry, Concordia University, Supervisor: Christine DeWolf
"In Silico Molecular Targets, Docking, Dynamics Simulation and Physiologically Based Pharmacokinetics Modeling of Oritavancin"

Omar Fliss,Food science,Université Laval,Supervisor: Ismail Fliss
"Resistance, Co-resistance and Cross-resistant to bacteriocins and antibiotics in Listeria monocytogenes"

DZ󾱲ҴDZ峾,Microbiology & Immunology,51Թ, Supervisor: Dao Nguyen
"Anti-Psl/PcrV bispecific monoclonal antibody improves bacterial clearance and reduces lung pathology caused by Pseudomonas aeruginosa isolates from cystic fibrosis children that failed eradication therapy"

Mark Hemmings,Biochemistry, 51Թ, Supervisor: Albert Berghuis
"Enzyme Mediated Aminoglycoside Resistance Without Target Mimicry"

վdzٳ,Biochemistry, 51Թ, Supervisor: Martin Schmeing
"Structural and Functional Studies of δ-Poly-L-ornithine Synthetases"

dz,Anatomy and Cell Biology,51Թ, Supervisor: Shuaiqi Guo
"In Situ structural analysis of Type IV Pilus priming complex assembly in Pseudomonas aeruginosa"

󳾲,Microbiology, INRS, Supervisor: Salim Timo Islam
"GfcD role in the Mechanism of Capsular Polysaccharide Secretion in E. coli Enteropathogenic (EPEC)"

ٲ,Infectious Diseases and Microbiology,51Թ, Supervisor: Alexander Lawandi
"In vitro exposure to non-antipseudomonal antibiotics (NAPA) induces Pseudomonas aeruginosa resistance to antipseudomonal antibiotics (APA)"

油ԻɲԻ徱,Medicine,51Թ[Flash Talk #1]
"Comparison of Mortality Burdens from Antibiotic Resistant vs Susceptible Infections in US Hospitals, 2018-2022""

Ჹᾱ,Animal Science,51Թ,Supervisor: Xin Zhao
"Zinc Oxide Drivers Plasmid-Mediated Antimicrobial Resistance Gene Transfer in Poultry-Associated Salmonella and E. coli"

ѳܱDZԻ,Microbiologie, infectiologie et immunologie,Université de Montréal,Supervisor: Yves Brun[Flash Talk #5]
"Identification and characterization of gene products with novel roles in outer membrane biology"

ܱ𲹳, Cell biology and anatomy, 51Թ, Supervisor: Shuaiqi Guo[Flash Talk #2]
"Structure and Function of TosA: A Key Virulence Factor in Uropathogenic Escherichia coli (UPEC)"

Ngoc SangNguyen, Microbiology and Immunology, 51Թ, Supervisor: Dao Nguyen
"The Evolution of Mammary Pathogenic Escherichia coli against the Colonization Resistance by Commensal Bacteria of the Bovine Udder"

岵',Food Science & Agricultural Chemistry,51Թ, Supervisor: Jennifer Ronholm
"A Fluorescence-Based Co-Culture Assay to Detect Antagonistic Interactions Between Bovine Klebsiella pneumoniae and Commensal Bacteria from Raw Milk"

Mohamed Elfateh Salem, Animal Science, 51Թ, Supervisor: Xin Zhao[Flash Talk #4]
"Antibacterial activities of peptide nucleic acids targeting Salmonella Penicillin‑Binding Proteins"

Anshu Saran,Anatomy and Cell Biology, 51Թ, Supervisor: Natalie Zeytuni[Flash Talk #8]
"Structural and Functional Insights into the Type-IX Secretion System's Response Regulator"

Marcus Simoes, Chemistry & Biochemistry, Concordia University, Supervisor: Brandon Findlay
"Conjugation of Plasmids into Environmental Bacterial Strains Induces Production of Antibiotics"

ʰԲԲ,Chemistry & Biochemistry, Concordia University, Supervisor: Brandon Findlay[Flash Talk #9]
"Influence of Growth Media on Collateral Sensitivity and Resistance in E. coli"

Գܳ,Animal Science, 51Թ, Supervisor: Jennifer Ronholm​​​​​[Flash Talk #10]
"Developing a Fluorescence-Based Co-Culture Assay to Discover Probiotic Candidates from Chicken Gut Bacteria as Alternatives to Antibiotics Against Avian Pathogenic Escherichia coli"

ٲԾղԳپԾ, Computer Science and Biology, Microbiology and Immunology, 51Թ, Supervisor: Jesse Shapiro[Flash Talk #7]
"Predicting antimicrobial resistance in Vibrio cholerae using resistance-associated sequence elements (RASE) software"

Seyed EhsanVasegh,Pharmacology and Therapeutics,Supervisor: Bastien Castagner
"Structure-Based Optimization of Small Molecule Therapeutics to Disarm Clostridioides difficile Toxins"

Elaine Wang, Biochemistry, 51Թ, Supervisor: Natalie Zeytuni
"The Bacterial Type V fimbriae: structure and function insights"

ѾԲ²Բ, Anatomy and Cell Biology, 51Թ, Supervisor: Shuaiqi Guo
"Molecular basis of V. cholerae adhesion to human cells"

Ѿ۲Բ, Anatomy and Cell Biology, 51Թ, Supervisor: Natalie Zeytuni
"Deciphering the Regulatory Networks Controlling Capsule Production and Immune Evasion in Porphyromonas gingivalis"

۳ܲ󳦳԰, Animal Science, 51Թ, Supervisor: Jennifer Ronholm
"Synthetic Microbiome Approach for Antimicrobial Resistance Studies in Agricultural Settings"

Abstracts by title:

A Fluorescence-Based Co-Culture Assay to Detect Antagonistic Interactions Between Bovine Klebsiella pneumoniae and Commensal Bacteria from Raw Milk
Bovine clinical mastitis, inflammation of the mammary gland, is associated with microbial dysbiosis. Klebsiella pneumoniae is a common cause of severe mastitis, leading to significant economic impacts in Canadian dairy farming. Enhancing colonization resistance by identifying protective commensals in the udder is a promising strategy, but bacteria with antagonistic activity against K. pneumoniae remain unidentified. To address this, we fluorescently tagged a bovine mastitis-derived K. pneumoniae strain (KP-RFP) using a Tn7-based chromosomal integration system. Raw milk from a healthy mammary gland will be enriched in broth, and single bacterial cells will be sorted into a 96-well plate using the B.SIGHT (Cytena). Each well will be co-cultured with KP-RFP, and its growth will be monitored via fluorescence. Wells with reduced fluorescence suggest potential antagonistic activity and will be plated to confirm antagonism. This high-throughput assay enables the rapid identification of milk commensals that suppress K. pneumoniae growth, informing microbiome-based mastitis prevention. Back to Bridget

​ċċċċċAntibacterial activities of peptide nucleic acids targeting Salmonella Penicillin‑Binding Proteins
Salmonella is widely known as one of the most critical enteric infectious pathogens worldwide, with a high incidence of multidrug resistance (MDR). The emergence and dissemination of multidrug-resistant (MDR) Salmonella strains restrict therapeutic choices and underscore the necessity for development of novel therapeutic approaches. Antisense peptide nucleic acids (PNAs) are synthetic DNA/RNA mimics. Antisense PNAs targeting essential genes have demonstrated the potential as therapeutic agents, as they effectively reduce the growth of various pathogenic bacteria. Peptidoglycan (PG) has historically been one of the central targets for antibiotics in the ongoing battle against pathogenic bacteria. In this study, based on the genome sequence of S. Typhimurium strain SL1344, a set of PNA conjugates with a cell penetration peptide (CPP), (KFF)3K, were developed to target three potentially essential genes; ftsI, which encodes penicillin-binding protein 3 (PBP3), mrcB, which encodes Penicillin-binding protein 1B (PBP1B), and mrdA, which encodes Penicillin-binding protein 2 (PBP2). These PNAs- CPP were evaluated for their antibacterial properties in vitro as well as in vivo. All three PNAs- CPP showed an antibacterial effect in a concentration-dependent manner. Among the three PNAs-CPP, anti-mrdA PNA-CPP showed the most potent inhibition in vitro and in vivo. The results were associated with selective inhibition of the targeted genes’ mRNA expression. Morphological analysis confirmed that the antisense inhibition of Salmonella targeted genes led to interference with the cell division and elongation. Consistently, treatment with these three PNAs-CPP increased the survival of adult larvae in a Caenorhabditis elegans infection model. These findings demonstrate that ftsI, mrcB, and mrdA are effective targets for developing antisense antibiotics. The outcomes of our study present a viable approach for addressing Salmonella infections using antisense-based therapy. Back to Mohamed Elfateh

Anti-Psl/PcrV bispecific monoclonal antibody improves bacterial clearance and reduces lung pathology caused by Pseudomonas aeruginosa isolates from cystic fibrosis children that failed eradication therapy
New-onset Pseudomonas aeruginosa (P.a) infections in cystic fibrosis patients are often treated with inhaled tobramycin (TOB), but eradication therapy fails in 10-40% of cases. Novel therapeutic strategies are thus needed. This study examined a bispecific monoclonal antibody (mAb) targeting Psl and the type III secretion system protein PcrV to enhance neutrophil (Nφ) mediated opsonophagocytic killing (OPK) in vitro and improve P.a clearance in vivo. The mAb was tested for its ability to enhance Nφ OPK of persistent P.a isolates in vitro. An in vivo P.a pulmonary infection model assessed the mAb's effect alone or with TOB on bacterial clearance. Results showed the mAb enhanced in vitro Nφ OPK of persistent isolates and that a prophylactic dose significantly improved in vivo bacterial clearance. Studies also suggest that combining the mAb with TOB further enhances enhance bacterial clearance compared to single modality therapy and that a post-infection administration with TOB can also be effective in reducing the pulmonary bacterial burden. Back to Sophia

Comparison of Direct Disc and Vitek2 Antimicrobial Susceptibility Testing on Positive Blood Cultures from Healthcare Facilities Across Quebec, 2020-2024
Background: Delays in antimicrobial susceptibility testing (AST) can lead to prolonged inappropriate empiric therapy and worse outcomes in bacterial infections. This study evaluated the performance of Kirby-Bauer (KB) disc diffusion directly from positive blood cultures, compared to the Vitek2© automated system, which tests isolated colonies.Methods: We retrospectively analyzed 25,504 positive blood cultures processed at the 51Թ Health Centre (MUHC) between January 1, 2020, and December 30, 2024. Antibiotic susceptibility results from direct KB testing were compared to Vitek2 results. Categorical agreement and error rates were calculated. Ordinal logistic regression identified pathogen-antibiotic combinations associated with increased error risk.Results: Categorical agreement was 94.2%. Minor, major, and very major error rates varied across organisms and antibiotics (ranges: 68.8%, 19.8%, and 11.3%, respectively).Conclusion: Direct KB testing shows high agreement with Vitek2 and may support faster AST reporting, though caution is needed for gram-positive organisms and non-beta-lactam agents. Back to Khlood

Comparison of Mortality Burdens from Antibiotic Resistant vs Susceptible Infections in US Hospitals, 2018-2022
Background: While antimicrobial resistance (AMR) is a major concern, infections from susceptible bacteria remain understudied. We assessed the burden of death from resistant versus susceptible bacterial infections in U.S. hospitals.Methods: We conducted a retrospective cohort study of adults with culture-positive bacterial infections in 285 hospitals (2018–2022) using the PINC-AI database. Resistance was defined by WHO/ECDC (MDR) criteria. Risk-adjusted mortality rates were calculated using predictive margins, and multiple imputation handled missing data.Results: Among 739,404 patients with 911,966 infections, overall mortality was 10.7%. Patients with AMR infections had more severe illness and received less effective initial therapy. Adjusted mortality was modestly higher for resistant infections (e.g., 11.1% vs 10.1% per WHO criteria). However, susceptible infections caused more deaths overall. For hospital-onset infections, having any infection increased mortality more from baseline than the additional mortality risk added on by resistance (aOR 1.41 vs 1.55).Conclusion: Despite higher mortality for resistant infections, susceptible infections cause more deaths and warrant greater focus in hospital infection prevention efforts. Back to Alexander

Compensatory Mutations and the Evolution of Reduced-costs of Resistance in Pseudomonas aeruginosa
The rise of antimicrobial resistance (AMR) among human pathogens requires novel treatment strategies to control infection. In Pseudomonas aeruginosa, spatially variable drug treatment can delay, but not prevent, the spread of resistance. Although resistance typically comes with fitness trade-offs, spatial heterogeneity gives rise to generalist resistant strains that have high fitness even in the absence of antibiotics. Here, we explore the role of second-site compensatory mutations in the evolution of reduced-costs of resistance. We identified mutations in a motility regulator gene, morA, that arose repeatedly under spatially variable treatment after mutations in known resistance gene nfxB, signifying a compensatory relationship. We quantified fitness in the presence and absence of antibiotics, revealing reduced-costs of resistance for strains with second-site mutations in morA. Our results point to morA as a target for future research in AMR, while also providing more detailed insight into the limitations of spatial heterogeneity as a treatment option. Back to Nick

Conjugation of Plasmids into Environmental Bacterial Strains Induces Production of Antibiotics
Antibiotic resistance has become increasingly commonplace in many pathogenic bacterial strains and a new method of finding antibiotics is needed to match the increasing demand. One potential method is to identify new antibiotics naturally produced by bacteria as secondary metabolites, used by bacteria to fend off other competing strains. However, bacteria tend to only express the corresponding biosynthetic gene clusters for many secondary metabolites under conditions of stress, not under ideal lab growth conditions. To increase secondary metabolite production and identify cryptic antibiotics we have induced intracellular stress, conjugating activator plasmids into a wide range of environmental bacterial strains. This has led to significant increase in the number of isolates producing antimicrobials. I have identified specific plasmid elements, such as gene insert length and genetic makeup, as well as media additives that have an impact on plasmid induced stress and secondary metabolite production. The impact on cellular stress and metabolite production was determined by LCMS and analysis of growth rates. The untapped biosynthetic potential of bacteria is vast, and through this work I will enable the exploration of their metabolome, allowing for the uncovering of new potentially life saving compounds. Back to Marcus

Deciphering the Regulatory Networks Controlling Capsule Production and Immune Evasion in Porphyromonas gingivalis
Porphyromonas gingivalis (Pg) is a keystone periodontal pathogen in periodontitis, a chronic inflammatory disease damaging tooth-supporting tissues. Pg’s rising resistance to antibiotics like gentamycin, clindamycin, and amoxicillin complicates treatment and highlights the need for new therapeutic strategies. Hyper-virulent Pg strains evade immune clearance by producing a K-antigen capsule, regulated by the HaeSR two-component system (TCS). Our research investigates how the HaeSR TCS mediates immune evasion and supports antibiotic-resistant persistence in the host. Specifically, we aim to identify the activation signal of HaeS, determine how HaeSR TCS regulates capsule synthesis, and also assess its overall impact on virulence of Pg. Biochemical and structural analyses confirmed heme binding to the HaeS sensory domain. Mutational studies elucidated the binding mechanism, and functional assays with a ΔHaeS strain showed reduced virulence. Together, our findings reveal how Pg senses host-derived heme to modulate virulence and suggest potential strategies to target antimicrobial-resistant Pg infections. Back to Mia

Developing a Fluorescence-Based Co-Culture Assay to Discover Probiotic Candidates from Chicken Gut Bacteria as Alternatives to Antibiotics Against Avian Pathogenic Escherichia coli
Avian pathogenic Escherichia coli (APEC) can cause serious disease in poultry, including septicemia, perihepatitis, and pericarditis, often leading to high mortality and economic losses. While disinfection and improved airflow offer some control, and vaccines are in development, concerns about antimicrobial resistance make it important to find alternatives to current antibiotics. One promising option is probiotics, which may reduce APEC colonization through competitive exclusion, bacterial antagonism, or immune modulation. To test this idea, I am developing a fluorescence-based, high-throughput co-culture assay to screen chicken gut commensals for anti-APEC activity. Using a Tn7 transposon system, I inserted the mScarlet-I gene into APEC for visual tracking of its growth. This modified strain will be co-cultured with unique chicken commensals and E. coli strains from our laboratory collection. Red fluorescence will be measured to assess APEC growth in each co-culture. Isolates that strongly reduce fluorescence will be considered novel probiotic candidates for Canadian poultry. Back to Jinha

Dynamic changes in Staphylococcus aureus Penicillin Binding Protein isoform profiles during growth and antibiotic exposure
Background: Staphylococcus aureus has the ability to persist in blood despite antimicrobial therapy. We theorized that adaptations in its PBP isoform profile may allow for antibiotic tolerance and prolonged infection.Methods: We used parallel reaction monitoring to perform relative quantification of the PBP isoform profile of Staphylococcus aureus across its growth curve, and after timed exposure to subinhibitory cefazolin.Results: Our assay could simultaneously detect and provide relative quantifications of PBP1, 2, 3 and 4. We found relative stability of the profile across the growth phases. Under antibiotic selection, there was a 100 fold increase in the concentration of PBP4.Conclusion: While the PBP isoform profile is stable across cell density and growth phase, cefazolin exposure causes an upregulation in PBP4 concentration which may allow it to tolerate antibiotic stress. Back to Khlood

Enzyme Mediated Aminoglycoside Resistance Without Target Mimicry
Aminoglycosides are a broad-spectrum, bactericidal class of antibiotics. Aminoglycoside acetyltransferases (AACs) inactivate aminoglycosides through acetylation. AACs, capture aminoglycosides in a low-energy conformation nearly identical to the binding mode seen in complexes of aminoglycosides bound to bacterial ribosomes, with the aminoglycoside central ring stabilized in chair conformation. This is termed “target mimicry.” We have solved crystal structures of AAC(3)-Ia and AAC(3)-XIa bound to aminoglycosides with their central ring stabilized in boat conformation. These are the first reported structures of resistance enzymes that do not display target mimicry. We hypothesized that these enzymes would have a lower affinity for aminoglycosides and that they likely provide less protection against antibiotic treatment. Through isothermal titration calorimetry and in vivo antibiotic susceptibility testing, we assessed the thermodynamic parameters of substrate binding and the practical implications of non-canonical aminoglycoside binding modes. These results provide deeper insights into the role of target mimicry in aminoglycoside resistance. Back to Mark

GfcD role in the Mechanism of Capsular Polysaccharide Secretion in E. coli Enteropathogenic (EPEC)
The Escherichia coli O127:H6 capsule is a key virulence factor, preventing host immune destruction. Classified Group 4 (G4C), its machinery includes GfcD, a novel predicted two-beta-barrel membrane protein. One barrel resembles polysaccharide secretion porins, the other amyloid-secreting porins. We hypothesize GfcD mediates inhibitable G4C secretion, stabilized by co-secreted amyloids. An improved Percoll gradient confirmed GfcD's necessity for G4C secretion, as G4C+ cells sedimented differently. Congo Red staining indicated more surface amyloids in wild-type than ΔgfcD cells. GfcD's AlphaFold structure underwent molecular dynamics in a simulated membrane, then virtual screening of over 600 FDA-approved drugs targeted its external face. Hits tested on wild-type cells, using Percoll gradient analysis, revealed four inhibitory drugs. These findings identify virulence factor machinery and suggest pathways for developing inhibitors to reduce bacterial virulence. Back to Ahmad

Harnessing Stress-Induced Biosynthesis for Natural Product Discovery
The rise of antibiotic resistance and the slow pace of new drug discovery have reignited interest in natural products (NPs), especially those produced by bacteria. However, the majority of biosynthetic gene clusters (BGCs) remain silent or cryptic under standard lab conditions, limiting our ability to access their full chemical potential. In this study, we explore plasmid-mediated stress as a strategy to unlock these hidden pathways and enhance NP production.Using Photorhabdus strains, we conjugated two plasmids, pARO190 and pARO190-NCI, into over 80 bacterial isolates and screened more than 200 resulting samples via spot-on-lawn assays against E. coli ATCC 25922 and B. subtilis DSM 10. We observed that plasmid carriage alone, particularly under stressful metabolic load, led to the induction of novel antimicrobial activity in strains previously considered silent. Strains such as Photorhabdus bodei CN4-25 and Xenorhabdus doucetiae DSM 17909 exhibited enhanced bioactivity post-conjugation.Fractions from selected cultures were purified and analyzed using flash chromatography and HPLC-DAD, revealing distinct peaks at multiple wavelengths and retention times, many correlating with zones of inhibition. This suggests the production of bioactive metabolites triggered specifically by plasmid-induced stress.Together, our findings support the use of conjugative plasmid transfer as a powerful tool to activate silent BGCs and uncover cryptic antibiotics, paving the way for expanded natural product discovery from microbial libraries. Back to Rayan

High-throughput tools to probe Salmonella-gut microbiota dynamics
To establish itself in the intestinal environment, Salmonella enterica serovar Typhimurium closely interacts with the host microbiota, thereby making it an excellent model organism for the study of microbial interactions within a context of infection. In this study, we found that S. Typhimurium becomes tolerant to azithromycin when co-cultured with lactobacilli strains. Acidified media from cell-free supernatant of lactobacilli for instance, also induced the tolerant phenotype. Using a collection of single-gene deletion mutants of S. Typhimurium, we were able to determine that in presence of the lactobacilli, the pathogen undergoes changes in its metabolism that leads to increased tolerance against the antibiotic that prevails the modification in envelope homeostasis and membrane permeability observed with acidified media. A second high-throughput assay will be carried, this time using a collection of S. Typhimurium promoters, in order to further investigate the transcriptional events that occur in the pathogen in presence of lactobacilli and azithromycin. The finding of this interaction highlights the importance to explore beyond the direct antimicrobial effect of antibiotics, emphasizing the broader microbial community complex. Back to Laurence

Identification and characterization of gene products with novel roles in OM biology
The outer membrane (OM) of Gram-negative bacteria acts as a protective barrier. Understanding more about OM biology is important for developing treatments against these pathogens. The goal of this work is to identify and characterize gene products with novel roles in OM biology. Genes of interest were identified through a screen of a knockout library in Escherichia coli with the fluorescent reporter N-phenyl-1-napthylamine. Hits of interest include knockouts of four different genes involved in thiamine synthesis, and two other genes of unknown function that are localized to the cell envelope. We are currently investigating these mutants further by testing sensitivity to other known OM-targeting treatments and using microscopy to track changes in the OM in these strains. These experiments will help elucidate the connection between these genes of interest and the OM, thereby improving our understanding of OM biology and offering insight into possible treatments against Gram-negative pathogens. Back to Emma

Implementation of a drug-discovery pipeline to identify polysaccharide secretion-blocking compound
Myxococcus xanthus secretes exopolysaccharide (EPS), biosurfactant polysaccharide (BPS), and major spore coat (MASC), each a sugar polymer produced by a parallel Wzx/Wzy-dependent pathway. The terminal component of each pathway has been already identified to be the integral OM β-barrel porins WzpX, WzpB, and WzpS. To probe the stability of the model structures of WzpX/B/S, each porin was subjected to molecular dynamics simulations. Virtual screening was carried out using a library of FDA-approved compounds to identify binders that could block each β-barrel porin and inhibit polysaccharide secretion. These compounds were tested for their ability to affect known EPS/BPS/MASC production and developmental phenotypes. Together, these data (i) Reinforce the notion of WzpX/B/S as the terminal pieces of secretion machinery, and (ii) provide important proof-of-concept that calculated deep-learning membrane protein model structures can be used for rapid drug screening applications, and so here for the identification of compounds found to abrogate polysaccharide secretion. Back to Antoine

In Silico Molecular Targets, Docking, Dynamics Simulation and Physiologically Based Pharmacokinetics Modeling of Oritavancin
Oritavancin is a semi-synthetic lipoglycopeptide antibiotic primarily used to treat serious infections caused by Gram-positive bacteria. The aim of this work was to investigate possible molecular targets, binding interactions, and pharmacokinetic profile of oritavancin. Existing computational methods were used. The results of pharmacokinetics showed that oritavancin is moderately solubility, and non-permeant of blood-brain barrier. Molecular docking results showed the highest binding affinity with PI3-kinase p110-gamma subunit (-10.34 kcal/mol), followed by Acyl-CoA desaturase (-10.07 kcal/mol) and Cytochrome P450 2C19 (-8.384 kcal/mol). Oritavancin PBPK modelling results showed that infusion has lower peak concentrations (Cmax) compared to bolus administration, with 1200 mg yielding 16.559 mg/L, 800 mg at 11.258 mg/L, and 200 mg over 3 days at 7.526 mg/L. Notably extended half-lives (t1/2) for all doses and slightly higher clearance rates compared to bolus, particularly for the 1200 mg and 800 mg doses. In conclusion, this study corroborated existing clinical pharmacokinetic evidence. Back to Toluwase

In Situ structural analysis of Type IV Pilus priming complex assembly in Pseudomonas aeruginosa
Many pathogenic bacteria (Pseudomonas aeruginosa, Vibrio cholerae, Neisseria gonorrhoeae, Legionella pneumophila, etc) use long cell-surface filaments called the type IV pili (T4P) to sense contact with surfaces and to initiate infections. Type IV pili are dynamic, surface-exposed filaments that play crucial roles in bacterial motility, adhesion, DNA uptake, and pathogenesis. T4P filaments extend and retract via an ATPase-driven motor complex considered one of the strongest biological motors. Despite detailed studies on individual components, how the T4P nanomachine assembles and functions in situ remains less well-understood, in part due to the difficulties in isolating the intact complex from the cell envelope. My research aims to resolve the in-situ architectures of the T4P nanomachines in P. aeruginosa using cryo-electron tomography (cryo-ET) with sub-tomogram averaging. In the P. aeruginosa T4P system, the tip of the extending pilus contains two key components. First, the non-pilin adhesin PilY1, has two distinct regions. While a von Willebrand Factor is localized to the N terminus of PilY1, which has been conserved in other species and is often important for adhesion, the PilY1 C terminus adopts a β-propeller fold. The second component of the P. aeruginosa T4P tip is comprised five minor proteins, FimU, PilV, PilW, PilX, PilE, and their genes are located in the same operon as pilY1. It had been proposed in previous research that PilY1 and the minor pilins form a “priming complex” and optimize the assembly of the entire machine. Here I aim to reveal the molecular basis of priming complex assembly and determine the minor pilin component that interfaces with PilY1. These findings will offer crucial insights into T4P biogenesis and may uncover novel targets for antimicrobial intervention. Back to James

In vitro exposure to non-antipseudomonal antibiotics (NAPA) induces Pseudomonas aeruginosa resistance to antipseudomonal antibiotics (APA)
Background: Antibiotic-resistant Pseudomonas aeruginosa is becoming more prevalent and severely limiting therapeutic options. Observational studies have linked the use of non-antipseudomonal antibiotics (NAPA) to the development of antibiotic-resistant P. aeruginosa. However, the mechanism underlying this observation remains unclear.Methods: We conducted an in-vitro directed evolution experiment where three strains of wild-type P. aeruginosa were grown in media containing NAPA, ertapenem, moxifloxacin, ceftriaxone, over fourteen days. Minimal inhibitory concentrations (MIC) to three antipseudomonal antibiotics (APA), meropenem, ciprofloxacin, ceftazidime, were measured periodically to see if the antimicrobial pressure of NAPA induced appreciable resistance to APA.Results: P. aeruginosa grown in media containing NAPA became more resistant to APA. The inducible rise in MIC was most pronounced when measuring MICs to APA within the same class of the exposure antibiotic. Ertapenem, moxifloxacin, and ceftriaxone conferred a maximum mean 29-fold, 11.8-fold, and 31.3-fold increase in MIC to meropenem, ciprofloxacin, and ceftazidime respectively. Cross-resistance between classes was equally observed.Conclusion: In-vitro exposure to NAPA confers inducible resistance to APA. Receipt of NAPA may be a risk factor for antibiotic-resistant P. aeruginosa, and should be taken into account when selecting empiric antipseudomonal therapy. Back to David

Influence of Growth Media on Collateral Sensitivity and Resistance in E. coli
Antibacterial susceptibility testing (AST) helps detect resistance and predict antibiotic efficacy, typically using cation-adjusted Mueller Hinton Broth (MHB) as the standard medium. However, such testing often overlooks the physiological conditions that influence antibiotic action in vivo. Urinary tract infections, among the most common bacterial infections, demand context-specific evaluations. In this study, we evolved nitrofurantoin-resistant E. coli ATCC 25922 mutants (n=16) using soft agar gradient evolution (SAGE) in MHB and artificial urine medium (AUM). SAGE enables gradual adaptation to antibiotics. AST of these mutants revealed higher minimum inhibitory concentrations in AUM than MHB for nitrofurantoin, levofloxacin, and trimethoprim. Notably, MHB-evolved mutants showed collateral sensitivity, while AUM-evolved strains exhibited cross-resistance. These results underscore the need to consider infection-site conditions when selecting media for AST to improve clinical relevance. Back to Prerna

Mapping the Morphological Landscape to Uncover Gene Function in Escherichia coli
A comprehensive understanding of E. coli gene function remains incomplete, with ~35% of genes lacking experimental validation. To address this, we used a CRISPRi library to knock down essential genes and examine resulting morphological phenotypes. The pooled sgRNA library was arrayed into individual mutants, validated by barcode sequencing, and screened in 384-well plates using phase-contrast and fluorescence microscopy. A subset of essential genes revealed six morphological categories: filaments, chains, spheres, long rods, short rods, and normal rods. Interestingly, genes with similar biological roles produced distinct phenotypes. For example, knockdown of translation-related genes fusA and thrS led to short cells, while rplM knockdown produced elongated rods. These findings highlight CRISPRi’s value in functional profiling, particularly for essential and uncharacterized genes. Future work will apply machine learning to refine phenotypic clustering and improve genome annotation. This morphological map may also support antibiotic discovery by revealing novel targets and signatures linked to critical cellular processes. Back to Sahar

Molecular basis of V. cholerae adhesion to human cells
The gram-negative bacteria Vibrio cholerae infects the intestinal mucosa and causes the severe diarrheal disease cholera, which has substiantial global mortality. The adhesin FrhA from V. cholerae promotes hemagglutination (HA), epithelial adhesion, and biofilm formation. However, the structure and function of the adhesin remains unclear. Here, we characterized the ligand-binding region of FrhA (FrhA-LBR), which contains a peptide-binding domain (PBD) and a carbohydrate-binding module (CBM). Hemagglutination assays confirm the dependence on PBD for HA and showed the inhibition of HA by peptide inhibitors. Cryogenic electron tomography data suggest that the PBD contributes to the formation of biofilm-like bacterial swarms around erythrocytes, yet V. cholerae can bind to erythrocytes through the CBM. Using X-ray crystallography, we resolved the FrhA-PBD structure at ~2.5 Å resolution, revealing the binding pocket in complex with peptide inhibitors. Our findings will inform the rational design of anti-adhesion therapeutics targeting RTX-family adhesins, with potential applications in preventing cholera colonization and infection. Back to Mingyu

Nucle.io: A rapid point-of-care diagnostic platform for bacterial identification.
With the support of the AMR Centre, we developed Nucle.io, a nucleic acid-based panel that detects, amplifies, and identifies bacteria and AMR sequences in one tube. By taking advantage of strand displacement reactions and DNA computing logic gates, our system allows for multiplexed diagnostic testing for multiple bacterial species and potentially AMR sequences at once within eight hours, nearly 1/6 of the time of status quo bacterial plates.Additional work performed with CRISPR-CasX (Dpb-Cas12e) enabled us to create both non-enzymatic and enzymatic signal amplification systems, providing flexibility in terms of temperature stability, limits of detection, and other parameters. In-silico modeling of strand displacement reactions performed alongside the project led to the creation of a standalone modeling system for winner-take-all and DPGA (DNA Programmable Gate Array) logic architectures with incorporated support for strand generation and system assembly instructions, creating a convenient platform for future DNA computing research. Back to Lucas

Phytoglycogen nanoparticles: a promising nanocarrier for the inhalation delivery of antibiotics
Lower respiratory bacterial infections have drawn a lot of attention due to their severe complications and the ongoing emergence of resistance to antibiotics. New strategies of antibiotic delivery are being explored to combat these infections especially through inhalation. Amikacin (AMK), an aminoglycoside antibiotic, exhibits an outstanding antibacterial activity; however, its use is limited due to low bioavailability and high toxicity. We report the use of biodegradable and non-toxic phytoglycogen nanoparticles for the inhalation delivery of AMK. Electrostatic association was employed for the loading of AMK into the carboxymethyl phytoglycogen. The nanoformulation shows a very high loading capacity and not only maintains the AMK antibacterial activity but also confers a biphasic release of AMK from the nanoparticles. Additionally, the formulation exhibits low cytotoxicity towards human lung cells. These data support phytoglycogen nanoparticles as excellent candidates for the inhalation delivery of antibiotics to treat bacterial respiratory infections. Back to Dalia

Predicting antimicrobial resistance in Vibrio cholerae using resistance-associated sequence elements (RASE) software
Antimicrobial resistance (AMR) is a critical global health threat, emphasizing the need for rapid diagnostics to guide appropriate antibiotic use and limit the spread of resistant pathogens. Vibrio cholerae, the bacterium responsible for cholera infections, contributes to this problem through horizontal gene transfer of resistance genes, driving ongoing multidrug-resistant outbreaks. Traditional phenotypic susceptibility tests are accurate but slow, often requiring days. This project evaluates the Resistance-Associated Sequence Elements (RASE) software for real-time, genomic-based AMR prediction in V. cholerae. A lineage-annotated reference database was constructed from 176 genomes matched with AMR phenotypes for ciprofloxacin, azithromycin and doxycycline. RASE was then benchmarked using Nanopore sequencing reads from 97 additional isolates. Lineage classification was highly accurate (BD-1: 100%, BD-2a: 96.4%, BD-2b: 88.2%) and AMR prediction also performed well (ciprofloxacin: 100%, doxycycline: 95.5%, azithromycin: 72.2%). Results were generated in under 30 minutes, demonstrating the feasibility of sequencing-based diagnostics for rapid outbreak response. Back to Daniel

Recycling Antibiotics: Tripartite Drug Cycling Reverses Antibiotic Resistance
Antibiotic resistance threatens to undo many of the advancements of modern medicine. A slow antibiotic development pipeline makes it impossible to outpace bacterial evolution, making alternative strategies essential to combat resistance. In this study, we introduce cyclic antibiotic regimens composed of three drugs or “tripartite loops” to contain resistance within a closed drug cycle. Through 424 discrete adaptive laboratory evolution experiments we show that as bacteria sequentially evolve resistance to the drugs in a loop, they continually trade their past resistance for fitness gains, reverting back to sensitivity. Through fitness and genomic analyses, we find that tripartite loops guide bacterial strains towards evolutionary paths that mitigate fitness costs and reverse resistance to component drugs in the loops and drive levels of resensitization not achievable through previously suggested pairwise regimens. We then apply this strategy to reproducibly resensitize or eradicate four drug-resistant clinical isolates over the course of 216 evolutionary experiments. Resensitization occurred even when bacteria adapted through plasmid-bound mutations instead of chromosomal changes. Combined, these findings outline sequential antibiotic regimens with high resensitization frequencies which may improve the clinical longevity of existing antibiotics even in the face of antibiotic resistance. Back to Farhan Rahman

Resistance, Co-resistance and Cross-resistant to bacteriocins and antibiotics in Listeria monocytogenes
This study aims to study and characterize the antimicrobial activity and resistance mechanisms associated with five antimicrobial peptides against 20 foodborne and clinical Listeria monocytogenes strains. Nisin Z, pediocin PA-1, plantaricin S, native brevibacillin and its synthetic analogue brevibacillin Thr1, have been used for their diverse structures and mechanisms of action. In vitro inhibition assyas showed notable bactericidal activity with MICs of 0.54–15.00 µM and MBCs of 1.08–60.00 µM. Resistant variants were generated by successive exposure to increasing concentration of each antimicrobial peptide and then characterized phenotypically and genotypically. No cross-resistance with conventional antibiotics was observed, but some co-resistance and cross-resistance between peptides were detected. A multidisciplinary approach combining whole genome sequencing and metabolic analysis identified genetic mutations and metabolic alterations associated with resistance, shedding light on the adaptive pathways of L. monocytogenes. Back to Omar

Screening and analysis of antibiotic production by Canadian High Arctic bacteria
With a dry research and development pipeline for antibiotics, researchers are exploring new avenues for identifying novel compounds to combat the current antibiotic resistance crisis. We propose to investigate bacteria from the Canadian High Arctic, an extreme environment with high microbial diversity and unique environmental pressures. The goal of this project is to develop a pipeline to screen Arctic isolates in search of novel antibiotics. We screened hundreds of Arctic isolates for antibacterial activity in coculture, followed by testing the activity of organic extracts from these isolates. Extracts from several candidate extracts were identified as having activity against multiple pathogens. Using Liquid Chromatography fractionation methods on one extract, we identified a potential compound responsible for bioactivity. We also identified the putative biosynthetic gene cluster responsible for synthesis of this compound. This work will help address the lack of novel antibiotics by searching for new compounds using isolates from understudied environments. Back to Eszter

Structural and Functional Insights into the Type-IX Secretion System's Response Regulator
Chronic periodontitis, a severe gum disease, is commonly treated with mechanical therapy and antimicrobials. However, rising antibiotic resistance in Porphyromonas gingivalis, a keystone pathogen, underscores the need for alternative strategies. The Type IX secretion system (T9SS), essential for virulence factor secretion, presents a promising therapeutic target. Here, we present a comprehensive characterization of PorX - a response regulator required for functional T9SS assembly. In vivo deletion of porX abolished virulence factor secretion, validating its therapeutic potential. Structural studies revealed a unique effector domain in PorX, resembling the alkaline phosphatase superfamily, suggesting a novel role in nucleotide or lipid signaling. Biochemical assays confirmed zinc-dependent phosphodiesterase activity, with a large active site suited for complex substrates. Uniquely, PorX dimerizes upon zinc binding, implicating it as a potential zinc sensor. These findings expand our understanding of T9SS regulation and establish PorX as a druggable target for mitigating P. gingivalis virulence and antimicrobial resistance development. Back to Anshu

Structural and Functional Studies of δ-Poly-L-ornithine Synthetases
Amino acid homopolymers, such as Ɛ-poly-L-lysine, are antimicrobial polymers which are currently being used in many countries as natural food preservatives. The enzymes that synthesize these polymers, are a special kind of nonribosomal peptide synthetase (NRPS) family enzyme termed poly-aminoacyl synthetases (PASs). They include two domains commonly found in other NRPSs plus a final unique, membrane embedded domain. Very little is known about their structures and mechanisms. To understand these enzymes, I expressed several PASs as recombinant proteins in E. coli and purified the most robust PAS samples. I characterized their activity and will determine the 3D structure of these unusual enzymes using cryo-electron microscopy. I will perform several complementary biochemical assays, and mutagenetic interrogation to fully reveal the mechanisms of action in these PASs. My experiments will lead to a deeper understanding of these enzymes and could allow their exploitation for overexpression of useful natural and new-to-nature homopolymers. Back to Timothy

Structural basis for allosteric regulation of the proteasome core particle
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), encodes a unique proteasome system that is essential for maintaining cellular homeostasis during infection, particularly in drug-resistant TB strains. The 20S core particle (CP), a 720 kDa complex, consists of four heptameric rings with α7β7β7α7 stoichiometry, where the α-rings control substrate entry and the β-rings harbor the proteolytic sites. While allosteric regulation of proteasomes is well-characterized in eukaryotes and archaebacteria, its role in Mtb is underexplored. We aim to identify potential allosteric hotspots within the Mtb 20S CP, which could be targeted by modulators to disrupt protein degradation in drug-resistant strains. Using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and cryo-electron microscopy (cryo-EM), we present novel structural insights into the active and inactive states of the 20S CP, focusing on conformational changes in helices near the catalytic site. These findings provide new avenues for targeting Mtb proteasomes to combat antimicrobial resistance. Back to Adwaith

Structure and Function of TosA: A Key Virulence Factor in Uropathogenic Escherichia coli (UPEC)
Uropathogenic Escherichia coli (UPEC) is the leading cause of uncomplicated urinary tract infections (UTIs). TosA, a large nonfimbrial adhesin of the RTX family, promotes UPEC colonization by mediating host adhesion, but its structural properties and host interactions remain poorly understood. We employed a multi-faceted approach to study the TosA ligand-binding domain (TosALBD), focusing on calcium-dependent folding, oligomerization, and future host target identification. Circular dichroism (CD) spectroscopy revealed that TosALBD unfolds in calcium-depleted conditions and refolds upon calcium addition, suggesting calcium-dependent stabilization. Analytical ultracentrifugation (AUC) showed that TosALBD exists in monomeric and dimeric forms, with shifts in distribution under EDTA treatment, implying a potential role for dimerization in folding or secretion. Successful cloning and expression of TosALBD pave the way for future interaction studies via ITC and SPR, and structural analysis by cryo-EM. These findings support a model where TosA folds extracellularly in response to calcium, enabling stable host interaction and contributing to UPEC virulence. Back to Julie

Structure-Based Optimization of Small Molecule Therapeutics to Disarm Clostridioides difficile Toxins
Clostridioides difficile (C. diff) is a bacterium that causes the most prevalent form of hospital-acquired infection. C. diff causes severe intestinal infections leading to diarrhea with potential complications, including pseudomembranous colitis. The most common treatments for C. diff infections are antibiotics. However, these drugs also eliminate beneficial gut bacteria that normally prevent colonization, leading to high relapse rates. Consequently, there is a pressing need for alternative therapies to combat C. diff infections (CDI). The toxins produced by C. diff are ideal drug targets, as they are the primary drivers of disease symptoms. Our lab has developed a therapeutic strategy based on analogs of the intracellular co-factor inositol hexakisphosphate (IP6) that can trigger premature toxin auto-proteolysis. The objective of my work is to synthesize improved IP6 analogs based on recent understanding of the interaction between IP6, and the toxin obtained by docking and molecular dynamic simulations. These efforts aim to enhance the affinity of the analogs while maintaining activity and solubility in physiological conditions with the long-term goal of advancing a novel therapeutic to clinical development. Back to Seyed Ehsan

Synthetic Microbiome Approach for Antimicrobial Resistance Studies in Agricultural Settings
Bidirectional exchange of environmental antimicrobial resistance (AMR) harboring bacteria between livestock and humans could contribute to a subsequent environmental AMR pollution through manure. The bovine manure contains microbial communities with complex interspecies interactions that affect AMR microbiome dynamics. Our primary objective was to isolate livestock core fecal microbiota that will be used to develop a model synthetic microbiome.We utilized a chemostat to conduct the enrichment of bacteria from two manure samples for four weeks followed with streaking them on various culturing media under aerobic and anaerobic conditions. We recover approximately 500 isolates based on colony morphology. We observed an isolation of more diverse species over prolonged incubation time. Metagenomics and taxonomic identification of isolated colonies is ongoing. Our data suggests that the chemostat system displays a significant potential for recovery of unculturable bacteria from bovine gut, as well as its application in comprehensive AMR studies in complex multispecies models. Back to Alla

The Bacterial Type V fimbriae: structure and function insights
Type V fimbriae are surface-exposed adhesive hair-like filaments present on many Gram-negative bacteria, including Porphyromonas gingivalis, a key pathogen implicated in periodontitis. The adhesive fimbriae are crucial for host cell attachment, immune modulation, and biofilm formation, contributing to persistence and antibiotic resistance. Structurally, fimbriae are composed of a polymeric shaft built from major protein. At the tip, three minor proteins form an adhesive complex. An outer membrane protein anchors and regulates assembly at the base. Despite components of Type V fimbriae has been described, the precise assembly mechanisms remain poorly understood. Here, we resolved the architecture of an intact native Type V fimbria using cryogenic electron microscopy. The near-atomic structure of the fimbriae shaft reveals a donor-strand exchange mechanism, where a C-terminal strand integrates into the preceding subunit’s groove, indicative of protease-mediated polymerization. These findings significantly enhance understanding of Type V fimbriae assembly and provide insights into their functions. Back to Elaine

The Evolution of Mammary Pathogenic Escherichia coli against the Colonization Resistance by Commensal Bacteria of the Bovine Udder
Infection of cow udders, bovine mastitis, is a major problem for dairy farmers. Raw milk microbiome studies have identified commensal Aerococcus urinaeequi and Bacillus pumilus associated with healthy udders. A. urinaeequi produces organic acids while B. pumilus releases antimicrobial compounds. Our in vitro tests showed these commensal species could resist colonization by mammary pathogenic Escherichia coli (MPEC), suggesting their potential use for reducing antibiotic reliance. However, the effects of continual pathogen-commensal bacteria interactions remain poorly understood. We experimentally evolve MPEC in 30 sequential competition assays with commensal bacteria to study the pathogen population response to putative probiotic treatments. The metabolic fitness and resilience against competition of 8 MPEC isolates from intermediate and endpoint populations will be examined using fluorescence markers to survey the degree of resistance, trade-off, and spread of beneficial mutants in populations. Most resistant endpoint isolates will be sequenced and undergo invasion-from-rare experiments to determine their ecological relevance. Back to Ngoc Sang

Zinc Oxide Drivers Plasmid-Mediated Antimicrobial Resistance Gene Transfer in Poultry-Associated Salmonella and E. coli
The intensification of poultry production has contributed to the spread of antimicrobial resistance (AMR), often driven by plasmid-mediated horizontal gene transfer (HGT) in pathogens such as Salmonella and Escherichia coli (E. coli). While antibiotics and heavy metals are known to stimulate conjugation, the impact of non-antibiotic additives like zinc oxide (ZnO) remains unclear. In this study, Salmonella and E. coli isolates from fecal samples at antibiotic-free poultry farms were screened for plasmid types and resistance phenotypes. In vitro assays showed that one E. coli isolate (1-C) transferred plasmids to E. coli 3F2, and ZnO enhanced this conjugation in a dose-dependent manner. In vivo confirmation was achieved using a Caenorhabditis elegans model. Transconjugants exhibited combined resistance to ampicillin, tetracycline, and streptomycin. Thiourea inhibited ZnO-induced conjugation, suggesting reactive oxygen species (ROS) involvement. These findings suggest ZnO may promote the horizontal spread of AMR, warranting further evaluation of its use in animal agriculture. Back to Haijiao

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