PRINCIPAL INVESTIGATOR
Michael Parkins, MD, MSc, FRCPC
- Professor in the Departments of Medicine and Microbiology, Immunology and Infectious Disease at the University of Calgary.
- Clinic Director of the Southern Alberta Adult Cystic Fibrosis Clinic of the University of Calgary Medical Clinics at the Foothills Medical Center in Calgary Alberta.
My scope of clinical practice includes; cystic fibrosis, infections in the immune compromised host and general infectious diseases. My research historically focused on the pathogenesis of cystic fibrosis and other suppurative lung diseases. More recently, we have focused heavily on wastewater-based surveillance - leveraging our Pan Alberta Network (spanning municipalities, and parts thereof, and high-risk facilities such as hospitals and shelters) across the Province for a wide variety of target analyses including respiratory and gastrointestinal viruses, emerging and endemic pathogens and antimicrobial resistance genes. In addition to the research themes from my laboratory I supervise many medical trainees on independent clinically relevant research projects. Our program is supported by research funding from CIHR, NSERC, CFI, PHAC, Genome Canada, Genome Alberta, NIH.
Contact information:
Michael Parkins
Phone: (403)220-5951
Fax: (403)270-2772
Email: mdparkin@ucalgary.ca
SR. RESEARCH ASSOCIATE & COORDINATOR
Nicole Acosta, PhD
My expertise lies at the intersection of clinical and environmental microbiology, focusing on understanding complex microbial communities and their impacts on human health and public health surveillance. I use molecular approaches, including next-generation sequencing and metagenomics, to study heterogeneous and polymicrobial samples from clinical and environmental sources.
I completed my PhD in Microbiology and Biotechnology at the University of Alberta. In my current research, I study the microbiome of individuals with cystic fibrosis (CF), exploring how microbial communities change over time, vary between cohorts, and respond to chronic therapies. My research aims to uncover links between microbial dynamics and patient outcomes, providing insights to support improved clinical management.
In recent years, I have expanded my research to wastewater-based surveillance, leading efforts to monitor respiratory viruses and antimicrobial resistance genes across hospital and community wastewater systems. My work combines longitudinal surveillance and statistical modeling.
Contact information:
Nicole Acosta
Phone: (403) 220-4215
Email: paula.acostaamador@ucalgary.ca
LAB MANAGER
Barbara Waddell, BSc
My experience as a research technician spans 22 years and involves a variety of microbial, molecular and cellular technics. My research focus In the Parkins lab started out strain typing bacteria in the CF airway. I help maintaining an extensive biobank with CF sputum isolates from many species and have typed many using PFGE and MLST. Allowing assessment of infection transmission and possible epidemic strains. Currently I am working to gaining NGS experience and skills such as library preparation and bioinformatics. Two other main projects that I am working on are: (1) CMV’s impact on CF patients’ disease progression and (2) SARS-CoV-2 Pan Alberta wastewater monitoring. For the SARS-CoV-2 wastewater monitoring project, I have been involved in project implementation and set up for the Parkins lab as well as research and development. Some aspects include SARS-CoV-2 RTqPCR and reporting for a range of sites across Alberta, RTddPCR and assay development for new targets and variants of concern.
Contact information:
Barbara Waddell Phone: (403) 220-4215
Email: bjmalber@ucalgary.ca
POSTDOCTORAL FELLOW
Zhaohui (Shaelyn) Xu
My research integrates microbial ecology, genomics, and bioinformatics to address critical challenges in antimicrobial resistance and improve infectious disease surveillance. I completed my PhD in Food Microbiology at the University of Alberta, where I studied microbial persistence, biofilm formation, and genomic mechanisms of antimicrobial resistance in food processing environments.
As a postdoctoral researcher, my work focuses on two main areas: 1) Population genomics and bioinformatics to investigate bacterial strain structure, evolution, and transmission in patients with bronchiectasis; and 2) Metagenomic and wastewater-based surveillance approaches to monitor antimicrobial resistance and emerging pathogens across both community settings and marginalized populations.
Contact information:
Zhaohui (Shaelyn) Xu Email: zhaohuishaelyn.xu@ucalgary.ca
POSTDOCTORAL FELLOW
Daniel Crowley
Contact information:
Daniel Crowley Email: daniel.crowley@ucalgary.ca
POSTDOCTORAL FELLOW
Melika Moradi
Chronic suppurative lung disease (CSLD) is driven by persistent airway infections that cause progressive lung damage and reduced quality of life. Current treatment remains largely empiric, despite substantial variation in patient response and the growing threat of antimicrobial resistance (AMR). My work aims to advance precision therapeutics for CSLD (CF/non-CF patients) by integrating pathogen genomics, host factors, antibiotic treatment patterns, and clinical metadata to identify predictors of treatment success and resistance evolution. Building on my PhD research developing novel antimicrobials for chronic P. aeruginosa lung infection, I'll apply genomics, bioinformatics, and machine learning approaches to uncover actionable markers that can guide individualized therapy. The long-term goal of this research is to support evidence-based treatment decisions that improve patient outcomes while limiting AMR.
Contact information:
Melika Moradi Email: melika.moradi1@ucalgary.ca
GRADUATE STUDENT
Archie Shchemialiou
I am a Master of Science student in Microbiology and Infectious Diseases at the University of Calgary, with a Bachelor of Science in Biological Science. As a laboratory technician in the Department of Pathology and Laboratory Medicine, I have developed expertise in molecular diagnostics and microbial analysis.
My thesis focuses on leveraging wastewater-based surveillance (WBS) to detect and quantify various strains of Streptococcus pyogenes and Streptococcus pneumoniae. I am using molecular techniques (e.g., qPCR and sequencing), in order to piece apart the various strain-types and characterize the strain-level diversity of these pathogens across Alberta populations. This work enables tracking of strain distributions that correlate with invasive disease burden and vaccine-driven shifts in pathogen populations.
Contact information:
Archie Shchemialiou
Email: artsiom.shchemialiou@ucalgary.ca
GRADUATE STUDENT
Marcos Moussallem
While completing my Bachelor of Science in Cellular, Molecular, and Microbial Biology at the University of Calgary, I worked externally in a research and development role for a biotechnology startup company. My work largely focused on the production of a rapid bacteria test, alongside composite water sampling and wastewater-based epidemiology. I am excited to continue my education as a Master of Science student in the Parkins laboratory where my knowledge in the fields of microbiology and wastewater-based epidemiology can be extended to my research. My project focuses on the limits of detection of target microbes in composite wastewater effluent samples on small and large scales, as well as bias towards different components and areas of a target facility. The main outcome of this project will be to aid future research in wastewater-based epidemiology by enabling a better understanding of the limitations of samples.
Contact information:
Marcos Moussallem
Email: marcos.moussallem@ucalgary.ca
FORMER STUDENTS
GRADUATE STUDENT
Julianna Svishchuk
Having completed my undergraduate degree in Cellular, Molecular, and Microbial Biology and the University of Calgary, I conducted my Undergraduate Honours Thesis at the Parkins Lab, studying inoculum effects of Staphylococcus aureus infections in the cystic fibrosis (CF) lung environment. I am thrilled to now be a Master's student with Dr. Parkins, my project shifting from a bacterial to a viral basis. Currently, my work focuses on the cellular and epidemiological nature of cytomegalovirus (CMV) lung infections in cystic fibrosis patients. Given the recent observation that CMV seropositivity is correlated with more rapid progression to end-stage lung disease in CF cohorts, the investigation of CMV's impact on CF disease progression is of high importance. The aims of my Master's project lie in studying the incidence and prevalence of CMV (and other herpesviruses) across CF cohorts, as well as potentially exploring the inflammatory profiles of CMV in airway eptihelial cells through an in vitro approach.
Contact information:
Julianna Svishchuk Email: jsvishchuk@ucalgary.ca
GRADUATE STUDENT
Lauren Bowron
The nature of the cystic fibrosis (CF) lung creates a welcoming environment for respiratory infections from opportunistic pathogens such as Pseudomonas aeruginosa. CF patients that acquire such infections often experience respiratory decline and a subsequent reduction in their quality of life. Consequently, understanding how to prevent infections from occurring in CF patients is crucial to ensure patient well-being. My research looks at using an integrated clinical and laboratory approach to study longitudinal changes in the lung microbiome of persons with CF and assess how we can use these changes to predict susceptibility to incident infections from classical pathogens like P. aeruginosa. Through this research, I am exploring the biomarker capabilities of the CF lung microbiome that correlate with bacterial infection and treatment response. My passion for translational research led me to the Parkin’s lab where I hope to produce meaningful and applicable results to benefit persons with CF. Outside of the lab, I have found passion in health advocacy and education through my volunteer work with AHS supporting cognitively impaired seniors and through my outreach role in the mental health organisation, Outrun the Stigma. My other interests include running, hiking, baking, and space exploration.
Contact information:
Lauren Bowron Email: lauren.bowron@ucalgary.ca
GRADUATE STUDENT
Emily Au
I am a recent Bachelor of Health Sciences graduate with specialization in Biomedical Sciences and conducted numerous microbiology and molecular biology research projects during my undergraduate studies. Due to my interest in translational research, I joined the Parkins Lab as a Master’s candidate. The main objective of my research is to adapt the SARS-CoV-2 wastewater surveillance tool to investigate antimicrobial resistance prevalence in tertiary-hospital populations to inform infection control and antimicrobial stewardship.
Contact information:
Emily Au
Email: emily.au1@ucalgary.ca
GRADUATE STUDENT
Conrad Izydorczyk
Respiratory failure due to repeated and chronic lung infections remains the leading cause of death for cystic fibrosis patients. A large component of CF standard of care guidelines focuses on preventing the acquisition of new lung infections by patients through a variety of infection prevention and control (IPC) practices. My work focuses on investigating the potential of various CF-associated pathogens (classical and non-classical) to transmit between patients in historic and current patient cohorts through the application of the latest bioinformatic methods in the field of infectious disease genomics/epidemiology, including (Bayesian) phylogenetics and molecular clock analyses, genomics/pan-genomics, and evolutionary analyses. The long-term goal of this work is to aid in the development of evidence-based approaches to IPC.
Contact information:
Conrad Izydorczyk Email: conradizydorczyk@gmail.com
Graduate students
UNDERGRADUATE STUDENT
Alex Buchner
My name is Alexander Buchner Beaudet. As an undergraduate researcher on the interdisciplinary University of Calgary wastewater-based epidemiology (WBE) team working in the Parkins lab, I am currently investigating the potential of utilizing WBE technology on other viral infections of epidemiologic significance (VIES) through an undergraduate honours thesis. Previously, I led a small wastewater sample collection cohort and was involved in the wastewater concentration protocol at the Advancing Canadian Wastewater Assets (ACWA) laboratory.
Contact information:
Alex Buchner
Email: alexander.beaudet@ucalgary.ca