Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Master of Science


Microbiology and Immunology

Collaborative Specialization

Molecular Imaging


Burton, Jeremy P.

2nd Supervisor

Goldhawk, Donna E.



Current microbial analyses to assess either the commensal microbiota or microorganism infection and disease typically require ex vivo techniques that risk contamination and are not undertaken in real time. The possibilities for employing imaging techniques in the microbiology field is becoming more prominent as studies expand on the use of positron emission tomography, ultrasound and numerous microscopy techniques. However, magnetic resonance imaging (MRI), a non-invasive in vivo modality that can produce real-time results is falling behind. Here, we examined the feasibility of detecting bacteria using clinical field strength MRI. Commensal, probiotic and uropathogenic Escherichia coli were scanned by 3 Tesla MRI where signal was related to the number of colony-forming units as well as total cellular iron and manganese content as determined by mass spectrometry. Various microbes commonly found in the human gut and urogenital tract were also assessed by MRI. Lactobacillus spp. displayed significantly higher transverse relaxation rates than other species, despite their low iron usage, potentially due to high manganese content. High MR relaxivity may enable detection of lactobacilli amidst host tissues, therefore, we assessed the potential to distinguish the MR signatures of two distinct cell types within mixed samples. With clinical field strength MRI, we were able to detect as few as ~26 x 106 colony-forming units of Lactobacillus crispatus ATCC33820 per mm3. In the future, MRI may allow for non-invasive evaluation of health or dysbiosis in the human microbiota as well as potential applications in tracking the dispersion and persistence of bacteria in broad applications from probiotic use, infection to tumour tracking.

Summary for Lay Audience

Background: Bacteria inhabit various niches throughout the human body. These bacteria can promote health, but in some cases specific bacteria can overgrow and be harmful to the host. We would like to use magnetic resonance imaging (MRI) to visualize and track these bacteria within their preferred environments to learn more about human-bacterial and bacterial-bacterial interactions in health and disease.

Hypotheses: Different bacterial types will appear differently on images from MRI. Adding the iron uptake gene magA to E. coli will make it easier to detect by MRI.

Methods: We imaged various bacteria and strains of E. coli found in the human gut and urogenital tract using MRI. We then cloned a gene (magA) which incorporates magnetic properties into an E. coli strain and then assessed its influence on bacterial MRI detection. We measured the concentrations of iron and manganese in all our bacteria since these metals can impact MRI. Finally, we imaged dilutions of Lactobacillus crispatus, a bacterium that we found to be very visible by MRI and mixed it with human bladder cells to see if we could distinguish the two cell types within a mixed sample.

Results and Significance: Different E. coli strains and bacteria have unique magnetic resonance signatures due to differences in metal content. In the future we hope to use MRI to identify and track bacteria within the human host.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.