Team:Lethbridge HS/Human Practices
Introduction
In Human Practices this year, we primarily focused on talking to experts that interact with either pathogenic bacteria or antibiotics on a regular basis. For us, it was important that we interview several people with similar roles (for example, a doctor and a pharmacist) because, although they may be similar in perspective, they may have different biases. These interviews aided us greatly in the development of our project, in helping provide feedback on our design, cater our project more to our stakeholders, and better understand the current situation of pathogenic bacteria detection and antibiotic resistance.
Ms. Kathy Bernard (Microbiologist)
The first human practices interview we conducted was with Kathy Bernard, a microbiologist at the National Microbiology Laboratory. We chose to interview Kathy as a starting point for our human practices season because our project is largely focused on the detection of pathogenic infection, and we wanted to get a better grasp of what methods are used currently. The focus that we had in conducting this interview was to learn more about the current, established methods of detecting pathogenic bacteria and the advantages and disadvantages of them.
Regarding which organisms she works with, Kathy told us she exclusively works with bacteria that have been known to cause disease in humans. She regularly performs tests to examine the properties of bacteria. We learned that, in her lab, a molecular approach to identifying bacteria is used frequently by sequencing and examining the genes of the various samples that are received. Another method that is used is examining the various properties of the organism, such as the biochemical properties, or examining the organism from directly within a patient’s specimens. A sputum sample may be sent to the lab and, with the help of specific primers, an agent can be recognized from within the sputum that is causing the infection, such as an agent that causes pneumonia. She also performs tests that determine the susceptibility of an organism to antibiotics. Kathy provided us with a general idea of the timeframes of these various tests. We learned that molecular testing can be done in several days , as a culture is required before testing. Biochemical tests can take longer, approximately a week to ten days, depending on the organism, while antibiotic susceptibility testing can take four days. Kathy also spoke about a new method of detecting these organisms in a rapid and accurate way: using mass spectroscopy, which can take only minutes to identify the sample. Upon questioning the lack of mass spectroscopy use as a widespread method of detecting infections in people, we learned that these instruments can cost upwards of $250,000. This is one of the major disadvantages of this method, as many facilities are unable to afford them for point of care testing.
Additionally, she informed us about a few roadblocks to pathogen detection. She described the issue of synergistic bacteria--bacteria that work together that cause infection, which makes it difficult to identify the type of infection. This helped inform our design as it helped us consider the scope of false positives and negatives that can occur, and in ensuring the specificity of our system. If there are multiple pathogens that are working together to cause an infection, then detecting which one is the most predominant, or diagnosing based upon the symptoms can be difficult.
We described our system to Kathy, who gave us feedback on the various nuances that may occur with it. For example, she pointed out the logistics of testing our therapeutic in a person, and the importance of making sure that our results are accurate.
“I think your theory is very intriguing and definitely worth pursuing [however] there is a long way to go before you reach clinical trials.”
Through this interview with Kathy, we were able to get an overview of the various methods of pathogen detection, as well as understand the roadblocks that may occur with using those methods, and detecting pathogens in general. This helped us understand the need for our project and the current condition of pathogen detection.
“Point of care technologies do exist, but they are not nearly as sophisticated or specific as CRISPR technologies could be. There are lots of them, but not for the same application [as your project] ”
Dr. Wong (Nephrologist/Internal Medicine)
Our team decided to interview a doctor because an individual in this profession could provide us with helpful input. Our goal was to determine how our detection strip and removal system could be employed in the healthcare system and what impacts our system would have on the healthcare field. In our first interview with Dr. Wong we learned of the criteria that doctors use when they are looking at prescribing antibiotics to their patients. Often times, if there are severe consequences of not treating a patient the doctor will prescribe empiric antibiotics. These are antibiotics that are prescribed to a patient based off of the symptoms a patient is displaying. In this prescription they will be using broad spectrum antibiotics, in order to target a larger range of possible infections. Antibiotics tend to fail when there is a misdiagnosis or if the patient is extremely frail. In these cases, either antibiotics are not required to treat the patient’s disease or the patient is too weak for the antibiotics to take proper effect. Following this interview our team learned that we needed to ensure that our system was effective, specific and would not cause any harm. We must ensure that the Cas-13a would only cleave the RNA of the target sequence, or else we may obtain a false result . In order to do so we looked further into some of the safety aspects of our system, such as increasing the length of the CRISPR RNA. As we progressed further with our project, more questions for Dr. Wong came up. We were curious if our test could be employed directly in a doctors office. We returned to him with some follow up questions. He believed that this test could be employed easily in a doctors office, but it depends on who controls the test. The test would be controlled by whoever was willing to pay for it. This would depend on the style of healthcare system run; whether or not the system is privatized or offers universal healthcare. According to Dr. Wong, currently there are not many tests that can be performed right in a doctors office. Therefore our system would provide the health care system with a mechanism that could effectively detect pathogens conveniently in the doctor's office.
Ward Eggli (EMS Resource officer)
Mr. Ward Eggli is an EMS Resource officer, who also sits in at various meetings, such as pathogen prevention, emergency medical services, audits and evaluates with Accreditation Canada for health care organizations across Canada which allows him to see various healthcare practices across the country. Our Goal in this interview was to be able to understand the challenges that paramedics are faced with on ambulance acquired illnesses and keeping their environment clean. Mr. Eggli expressed his concerns in making sure that ambulances are as clean as possible and through a partnership with the University of Lethbridge they have done DNA testing and sampling to prove that there are high quantities of nasty pathogens present. One of the studies that they found identified Clostridioides difficile on paramedics, at ten times the normal amount compared to the average person.
“So, they were actually carrying it, they believed. Ten times the normal amount. Now, that concerns us a ton; where are they getting it from? How long is it staying on them? Is it affecting them? And are they passing it along? That’s scary to us.”
He also expressed how part of a paramedics job is to access the environment that they are called to:
“The environment that our staff could be in would be in a patient’s home, they could be in a ditch, they could be on a rooftop, they could be in hospital, they could be in an office building, it’s just absolutely any place a patient might be picked up by ambulance is the environment that our staff need to navigate in a clean fashion.”
Mr. Eggli expressed that the biggest disadvantage that paramedics have today is keeping the ambulance clean. They do have a post-clean process for the back of an ambulance, but mostly for what they can see.
“It’s been conversation that we’ve had with the University of Lethbridge researchers is to develop in the future something that looks like a paramedic in a lab coat. So I can go on a call, I might even be able to in the future sample, scan my patient and say they have something in a rapid fashion, but also what’s potentially left behind that could be passed on to other practitioners, or other patients in the back of the ambulance, and that’s the whole flow of the hospital acquired infection, or in EMS, Ambulance acquired infection that could be passed on to somebody else that’s immunocompromised or just in a state that makes them more susceptible to the distribution of that pathogen.”
Chad Baker (Pharmacist)
Our human practices team had the pleasure of interviewing pharmacist Chad Baker of Southgate Medical Center. Our goal in interviewing Mr. Baker was to gain a deeper knowledge on broad-spectrum antibiotics and other, more specific antibiotics. He was also able to communicate his concern of how antibiotics could become completely ineffective in the near future. This of course poses a great issue to pharmacists as it limits their ability to prescribe anything for pathogenic related infections. Mr. Baker was able to give us a rough estimate of the amount of antibiotics they give out yearly, saying it ranged from 700 to 1200 antibiotics for their pharmacy alone. Most of these antibiotics are broad-spectrum as in some cases like bronchitis, doctors will most often prescribe antibiotics based on symptoms they observe. Doctors will most often order a culture in cases where a urinary tract infection is present which Mr. Baker mentioned could take multiple days. This wait time in some cases is not always an option and more immediate care is required. He also mentioned that a lot of the patients they receive at the pharmacist are very persistent to receive antibiotics immediately as it can make them feel more secure in fighting their infection. This of course puts a lot of pressure on pharmacists. After explaining our project to Mr. Baker, he believed that our solution would be able to provide that sense of security to patients as it would be immediate detection, and this in turn would take some of the pressure off of pharmacists.
Evangelia Vamvaka
(Postdoctoral Research Scholar)
A few members of our team were able to get ahold of Evangelia Vamvaka, a Postdoctoral Research Scholar at the Innovative Genomics Institute (IGI) at UC Berkeley. Dr. Vamvaka has worked with CRISPR technologies in plants before and so she was more familiar with the technology we were using than some of the other professionals we had talked to. We expressed the concern of off-targeting that was prevalent within the scientific community to Dr. Vamvaka.
“How you design your guide RNA strand and the length of it will ensure that no off-targeting occurs.”
She was able to answer our question by telling us that the specificity of our guide RNA depended on how we designed it and how long we designed it to be. The longer the guide RNA strand, the more specific it is. Dr. Vamvaka also mentioned that the stigma towards genetic engineering especially in Europe was huge and that the general public was more accepting of genetic engineering in plants than in humans. She was able to assist us in our approach of explaining the project, making sure that we clarified that we were not doing any gene editing with our Cas13a. A concern of ours was whether Cas13a would be able to survive long in the human body and she assured us that It would last long enough to fulfill its duty. We were very fortunate to get the opportunity to speak to her as she was able to answer many of the questions we had due to her history with CRISPR Cas technologies, and she asked us many questions about our project which has guided us in informing our project design.