Select Page
Dr. Michelle Alfa

Dr. Michelle Alfa

Principal Investigator
Infectious Diseases, Canadian Centre for Agri-food Research In Health and Medicine

Medical Microbiology, University of Manitoba

Research Focus

The Infectious Diseases Lab focuses on research in the area of Hospital Acquired infections. The three primary areas of research interest include:

  1. Clostridium difficile infections: spore reservoirs in the healthcare environment
  2. Medical device associated infections: role of cleaning errors in infection transmission
  3. Role of the Gut Microbiome in health of the elderly

The project related to C.difficile targets development of interventions that can break the cycle of transmission from spores of C.difficile in the environment that act as a reservoir. The project related to medical device infections is related to improving the efficacy of cleaning and preventing biofilm buildup in medical devices such as flexible endoscopes. The project related to gut microbiome is to investigate whether prebiotics can increase the diversity of the gut microbiome in the elderly providing them with better gut health.

Why is this work important?

Currently hospital acquired C.difficile associated disease (CDAD) affects more people than all other enteric bacteria combined. CDAD is most commonly hospital acquired, but it can also be community acquired. Approximately 25% of patients who develop CDAD will have a recurrence of their infection after treatment is stopped. The increased length of hospital stay, along with adverse outcomes (especially in elderly patients) and possible death make this a significant pathogen that we urgently need to control and develop alternative therapeutics that will be effective in either preventing or curing this serious infection.

Infections associated with improperly reprocessed medical devices are not common – but when they do occur – they often affect a large number of patients. Flexible endoscope procedures are becoming very wide-spread (e.g. colonoscopy to evaluate patients for rectal cancer) as such any problem associated with a flexible endoscope could potentially affect a large number of people. Since you cannot see inside the endoscope channels – it is important to ensure that the reprocessing is being done properly and that the device is truly safe to use on the next patient. Flexible endoscopes cannot be steam sterilized so other methods are used for disinfection that do not provide a wide margin of safety. Ensuring these medical devices are safe for use on patients is an important focus to ensure patients do not lose confidence in the medical system.

The gut microbiome changes from about 60 years onwards become less diverse in terms of microbes with resulting inability to digest resistant starches. The clinical study in conjunction with Deer Lodge will determine if “elder-specific” food products containing prebiotics may lead to increased gut microbiome diversity and better gut health (i.e. protection from infections).

What techniques and equipment are used in this laboratory?

Our lab has developed and utilizes tissue culture assays to evaluate the biological activity of C.difficile Toxin A and Toxin B. In addition, we utilize the “human gut” model to follow the impact of the microbial ecosystem on maintaining control of C.difficile replication and toxin production. In addition a number of molecular assays are used that include PCR, PFGE and sequencing.

For the medical device studies we have a wide range of narrow lumen reprocessors and flexible endoscope reprocessors that are used for our studies or are under development. The use of the MBEC pin model to study biofilm buildup has provided a valuable approach to understanding lack of disinfectant efficacy against microbes embedded in biofilm buildup.

Staff in the research centre working on Dr. Alfa’s research projects include: Nancy Olson, and Brenda-Lee Murray.

About Dr. Michelle Alfa

Dr. Alfa undertook her B.Sc. in Microbiology from the University of Manitoba, her M.Sc. in Microbiology at the University of New South Wales in Sydney, Australia and her Ph.D. in Medical Microbiology at the University of Alberta. She is board certified as a Clinical Microbiologist with the Canadian College of Microbiologists. She is currently a Professor in the Dept of Medical Microbiology at the University of Manitoba and Principal Investigator at the St. Boniface Research Centre.

Dr. Alfa has been involved in the teaching of undergraduate students, graduate students and, medical students for over 20 years. She has been awarded outstanding teacher awards as well as the “Distinguished Microbiologist” award from the Canadian College of Microbiologists. Dr. Alfa has over 100 peer-reviewed publications and book chapters and holds a USA patent for an artificial test soil that she developed. Dr. Alfa has also provided numerous National and International presentations on her research findings.

For more information, contact:

Dr. Michelle Alfa
Tel. (204) 235-3498

In Detail


Hospital acquired infections (HAIs) pose a significant challenge within healthcare. The main routes of transmission within healthcare includes patient to patient, hands of healthcare providers to patient and environment to patient. Of these transmission modes, there is ample evidence that the environment within healthcare facilities is a significant source (reservoir) for HAIs related to acquisition and infection by methicillin-resistant Staphylococcus aureus (MRSA), vancomycin resistant enterococci (VRE) and Clostridium difficile. Of these HAIs, C.difficile is the most challenging to eradicate from the environment as it forms spores and can survive on environmental surfaces for years. In addition to the environment as a reservoir for HAIs, medical devices can also act as reservoirs for infection transmission. Recent reports in Europe and North America have documented transmission of carbapenem resistant Gram negative organisms from contaminated endoscopes that have resulted in outbreaks and high rates of transmission that resulted in carriage of these multi-resistant organisms. The research in the Infectious Disease laboratory focuses on prevention of HAIs derived from exogenous sources such as the patient-care environment or contaminated medical devices.

A crucial aspect of infectious disease in humans is the status of the gut microbiome. We have more microorganisms in our gut that we have human cells in our body! The health of the gut microbiome plays a major role in warding off infections. The gut microbiome of humans changes and becomes less diverse at around 60 years of age. This “senescence” of the human gut microbiome in the elderly has relevance to HAIs because the changes in the gut microbiome of elderly patients often makes them more susceptible to developing infections such as C.difficile. The Infectious Disease research laboratory is involved in clinical evaluations to evaluate whether prebiotics can lead to a more balance gut microbiome in the elderly population and reduce their risk of infection.

Environmental-Associated Infections:

In order to eliminate the patient-care environment as a source of HAIs, our research is aimed at investigating optimal approaches to environmental disinfection that will ensure housekeeping compliance with application of disinfectant products as well as killing of relevant microorganisms. We have developed novel test methods to ensure the in vitro lab testing we perform reflects the challenges that disinfectants will be exposed to during use including; short exposure time (< 3mins), organic material and drying onto surfaces. In addition we use a range of test organisms that spans the range of organisms including Gram negatives and Gram positives, fungi and spore forms. Traditional disinfectants that are commercially available are evaluated as well as novel compounds developed by collaborative research groups. These compounds are evaluated not only in vitro in the laboratory but we also undertake clinical evaluations within the healthcare environment. This research helps manufacturers determine the efficacy of new and existing disinfectants and also helps healthcare identify the appropriate products that will lead to reductions in HAIs.

Medical Device-Associated Infections:

The majority of infections after surgical or diagnostic procedures are endogenous and are caused by the patients’ own microorganisms derived from their skin or mucous membranes. However, there are infections that arise from exogenous sources such as contaminated medical devices. These exogenous infections are preventable because reprocessing of medical devices should ensure that the device is safe for the next-patient use. Our research is aimed at investigating the role that improper cleaning and biofilm development play in medical device-associated infections. We have developed test models that mimic the type of build-up biofilm that can develop in medical devices. This allows us to realistically assess reprocessing monitoring methods that will ensure that any devices that are improperly cleaned are detected early and can be re-cleaned prior to disinfection and use on another patient. Our research is aimed at developing realistic rapid testing methods to ensure adequacy of cleaning and dry storage as well as clinical studies to demonstrate that the test methods developed can be reliably utilized in healthcare settings. Our studies identify areas that need to be improved for national guidelines and provide independent data for Infection Prevention and Control healthcare personnel to focus their efforts on to reduce the risk of medical device-associated infections.

Human Gut Microbiome:

The elderly human population (i.e. > 70 yrs of age) is under-evaluated in terms of how to prevent infectious diseases. Our research is aimed at better understanding the gut microbiome changes that occur in the elderly and determining if there is an opportunity to develop elder-specific food supplements that may reduce or eliminate the microbiome senescence that occurs. We have a collaborative research program with Deer Lodge that allows us to undertake clinical studies to determine if prebiotics that are consumed daily can change the composition and diversity of the gut microbiome in the elderly. These clinical studies also involve 30-50 year olds as a comparator group. These studies have great relevance as the proportion of the elderly within the population is expected to significantly increase over the next 10 years.


Alfa MJ, Olson N, Murray BL. Comparison of clinically relevant benchmarks and channel sampling methods used to assess manual cleaning compliance for flexible gastrointestinal endoscopes. Am J Infect Control 2014 Jan; 42(1):e1-5.

Alfa MJ, Olson N. Comparison of washer-disinfector cleaning indicators: impact of temperature and cleaning cycle parameters. Am J Infect Control 2014 Feb;42(2):e23-26.

Gawaziuk, JP, Alfa MJ, Olson N, Logsetty S. Intermediate-level disinfection with accelerated hydrogen peroxide prevents accumulation of bacteria in Versajet™ tubing during repeated daily debridement using simulated-use testing with an inoculated pork hock. Burns 2014 May; 40(3): 460-465.


Alfa MJ, Fatima I, Olson N. Validation of ATP to audit manual cleaning of flexible endoscope channels. Am J Infect Control 2013 March; 41(3):245-248.

Alfa MJ, Fatima I, Olson N. The ATP test is a rapid and reliable audit tool to assess manual cleaning adequacy of flexible endoscope channels. Am J Infect Control 2013 March; 41(3):249-253.

Alfa M, Olson N, Buelow-Smith L, Murray BL. Alkaline detergent combined with a routine ward bedpan washer disinfector cycle eradicates Clostridium difficile spores from the surface of plastic bedpans. Am J Infect Control 2013 April; 41(4):381-383

Walkty A, Lagace-Wiens PRS, Manickam K, Adam H, Pieroni P, Hoban D, Karlowsky JA, Alfa M. Laboratory diagnosis of Clostridium difficile infection – evaluation of an algorithmic approach in comparison with the Illumigene® assay. J Clin Microbiol 2013 April; 51(4):1152-1157.

Manickam K, Karlowsky JA, Adam H, Lagace-Wiens PR, Redina A, Pang P, Murray BL, Alfa MJ. CHROMagar orientation media reduces urine culture workload. J Clin Microbiol 2013 April; 51(4):1179-1183.

Trajtman AN, Manickam K, Macrae M, Bruning NS, Alfa M. Continuing performance feedback and use of the ultraviolet visible marker to assess cleaning compliance in the healthcare environment. J Hosp Infect 2013 April; 84:166-172.

Alfa M. Monitoring and improving the effectiveness of cleaning medical and surgical devices. Am J Infect Control 2013 May; 41 (5 Suppl):S56-S59.

Alfa MJ, Sepehri S. Combination of culture, antigen and toxin detection, and cytotoxin neutralization assay for optimal Clostridium difficile diagnostic testing. Can J Infect Dis Med Microbiol 2013 Summer; 24(2):89-92.

Al-Fifi, YSY, Sathianathan C, Murray BL, Alfa MJ. Pets are “Risky Business” for patients on Continuous Ambulatory Peritoneal Dialysis (CAPD). Can J Infect Dis Med Microbiol 2013 Fall; 24 (3): 96-98.

View on Mendeley

View on Scopus


Health Administration Award; Doctors Manitoba, 2011.

Teacher of the Year Award for Graduate Students, Dept. of Medical Microbiology, 2007-08.

Innovation Award; University of Manitoba, March 2006.

Distinguished Microbiologist Award; Canadian College of Microbiologists, April 2005.

Most Outstanding Teacher Award; For Med I Class of 1996-1997, from the Manitoba Medical Students’ Association.

Most Outstanding Teacher Award; For Med I Class of 1995-1996, from the Manitoba Medical Students’ Association.

Funding has been received for a wide variety of research projects related to medical device reprocessing and cleaning monitoring from Virox Industries, 3M, Serim Research Laboratory, Olympus Inc, and STERIS.

Many of these research projects are confidential, so specific details are not listed.


Life In the Lab