Team:Lethbridge/Integrated Practices

Lethbridge iGEM 2016

Integrated Practices

We incorporated feedback from the Lethbridge EMS and Fire department to directly influence our design strategy.

The University of Lethbridge iGEM team was approached by our local Fire and EMS department regarding a problem related to safety and cleaning standards in ambulances. Ambulances are the point of contact between sick patients and the hospital, and they have the potential to be reservoirs of pathogens. The incidence of multiple antibiotic resistant pathogens is on the rise which has led to an ongoing reassessment of cleaning standards in order to best prevent transmission. After every patient, only visible bodily fluids are cleaned, and deeper cleans of the ambulance occur once a month. However, it is unknown whether reservoirs of potentially virulent pathogens exist that are not visible to the naked eye, or whether current cleaning products are doing what they claim. With the current cleaning method it is possible that pathogens are being spread to hospitals, or other places in the community.

Our team consulted current literature in order to determine the best approach for our study. We found no studies in Canada, and from the global studies we were able to pinpoint sample locations and sampling techniques. All of the studies used cell culturing as their method of sample analysis, and found consistent results for pathogens identified.

In order to design something that would be practical and beneficial for the EMS to implement, and assess the real world applications and implications of our project, we met with first responders and participated in ride alongs. Before and after the ride alongs we surveyed first responder’s to get a better understanding of what areas they felt would be the dirtiest in the ambulance. With this new information, we developed a novel approach to assess the vehicle microbiome and monitor cleaning processes, the first of its kind in Canada.

Once we determined sampling locations, we designed a two pronged approach to help solve this problem with specific design criteria in mind. Our design strategy involved the following principles: 1) comprehensive; provide a complete picture of the vehicle microbiome, 2) portable; an easily accessible tool that could be transferred to different vehicles, 3) easy to use; no additional training would be required of the first responders, 4) standardized; develop protocols and methods that could be duplicated by others for similar or related applications, 5) rapid; first responders could quickly identify pathogens, and 6) specific; accurate in regards to the types of pathogens identified and detected.

Based on our design criteria, our team developed a single domain antibody library and custom bacterial-two-hybrid selection system to identify sdAb variants that recognize human pathogens. We sequenced our samples collected from the ambulances using the cutting edge MinION sequencing from Oxford Nanopore Technologies. We then surveyed the results of our findings and identified opportunistic pathogens (such as Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus faecalis, Prevotella intermedia), human commensals, and uncultured bacteria. The results of the microbiome sequencing influenced our choice of targets to select single domain antibodies against. These antibodies would be used in the design of an antibody based detection method to allow first responders to quickly identify the presence of harmful microbes, in turn allowing for the assessment of cleaning standards.