From analyzing drug-resistant bacteria on dairy farms in California to tracking unresolved foodborne outbreaks across the U.S., Candace Cole, Ph.D., a postdoctoral bioinformatics fellow at the Centers for Disease Control and Prevention (CDC), is on a quest to leverage microbiology to support food safety.
As a child, Cole proudly declared, "I'm going to be a scientist." While watching episodes of CSI: Crime Scene Investigation, Cole was captivated by the dramatization of forensic science experiments. "I just knew that was a career path I could follow," she said. "I was seeing scientists, doing work in a cinematic sense, and [being exposed] to the day-to-day work [performed] by scientists, which is something that, up until then, I really had no idea what that meant. That was a big turning point for me."
Throughout high school, Cole prioritized taking extra science classes, and by the time she got to California State University, Northridge (CSUN), she was set on majoring in biology. But an upper division immunology class helped Cole realize that she wanted to be more involved in research. "My immunology professor highlighted current research, and we learned lessons about how research is being applied to different topics that we were studying in immunology," she recalled. "It also helped that she was openly gay. [I could see] openly gay scientists doing research. I could see myself doing that, because she's doing it."
Cole, who identifies as a lesbian and Mexican American, remembers encountering only a few scientists early in her career who identified similarly to herself. "[Now] I see openly gay scientists all the time, but starting out, not really," Cole recalled. "You [feel like you] can't be what you can't see, and seeing people who were openly gay and doing research being successful, that was really helpful."
Throughout her undergraduate and graduate education, Cole harbored anxiety about sharing her identities publicly for fear of how she might be perceived or treated differently. "Five years ago, I stopped doing that. I got to a point where I thought, 'I am who I am; I'm not going to hide it anymore,'" she said. "Having those people who identified similarly to me in my programs did allow me to open up parts of myself, but it took me a while. And once I was open with who I was, I felt a lot better. I didn't face any backlash, but I will say that if there were more openly queer professors around me, then maybe I would have not felt the way I did for so long."
At CSUN Cole also noticed that, while a large portion of the school's students identified as Latine, she saw few to no Latine students in her STEM courses. In some cases, "it was really just me," she said. But the work at University of California (UC), Merced, where Cole would eventually earn her Ph.D., to increase and maintain a diverse student body was encouraging to Cole, and this is something she wants to see across all higher education.
"Shoutout to UC Merced for being a Hispanic-serving institution and doing the work to maintain that learning environment for the students of the Central Valley, as well as the rest of California," Cole said. "I see these students who say, 'I want to be a doctor,' or 'I want to be a scientist,' or 'I want to be a microbiologist.' UC Merced really offers a lot of opportunities for students to engage in research early on as an undergraduate student, and they're implementing a high school program now to get students into the UC system and get a college degree."
After undergrad, Cole was firmly on the research track and went on to pursue her master's degree in quantitative and systems biology at California State University, East Bay (CSUEB). "I just kind of happened across microbiology," she said. Cole joined a water-quality project looking at how microbes break down mercury in a post-mining watershed area and, eventually, took a microbiology course with a professor who would become her master's adviser. "It was really cool learning about microbes and the different things that they do in terms of breaking down waste in their environments-there's just so much to explore," Cole said. "I had a really great adviser who inspired me to find what I liked about microbiology."
Following a deeper exploration into microbiology, Cole was eager to return to immunology. "I really fell in love with immunology," she said. Yet, while pursuing her Ph.D., Cole didn't find working in an immunology laboratory to be the right fit. "Eventually, I found my way back into an antibiotic resistance lab-I felt right at home," she said. "Again, I had a great adviser who allowed me to explore the things I wanted to, and I got really into studying the mechanisms and evolution of antibiotic resistance, as well as being able to consider public health implications."
For her Ph.D., Cole examined antimicrobial resistance (AMR) trends in Merced, Calif., with a particular focus on agriculture in the area. "That was my segue from microbiology into the intersection between microbiology and public health," she said. The research team began by analyzing urinary tract infection (UTI) isolates from a local hospital. The samples revealed a heightened presence of AMR in the region. This prompted the question, "What is going on in Merced?"
Sitting in California's Central Valley, Merced County's top industry is agriculture. With the abundance of food production in the area, Cole and her fellow researchers took note of the widespread use of antimicrobials to boost crop growth and prevent infections among livestock. While antimicrobials can help produce successful yields, their pervasive use can lead to drug-resistant bacteria, which can be transmitted from crops and animals to humans.
With this in mind, the research team gathered soil samples from dairy farms to look for drug-resistant genes. "We did end up seeing that there were a lot of uropathogenic indicative genes, and there were similar antibiotic resistance genes or trends as what we had seen from our hospital collection," Cole explained.
While efforts are in progress to help mitigate the spread of AMR throughout agricultural practices, public awareness is limited. "It's not something that a lot of people really talk about outside of having organic food or not," Cole said. She hopes similar studies will boost recognition and an understanding of the threat of AMR, as well as signify a need for more sustainable agriculture techniques.
Now, as an Association of Public Health Laboratories (APHL)-CDC bioinformatics fellow, Cole is focused on tackling foodborne outbreaks, from Salmonella and E. coli to noroviruses. As a part of the Culture Independent Metagenomic Subtyping Team within the Enteric Diseases Laboratory Branch at the CDC (work funded through the Advanced Molecular Detection Program), Cole and her colleagues are invested in addressing gaps in outbreak investigations (which can ultimately lead to gaps in surveillance). Currently, shotgun metagenomic sequencing, where researchers can examine all genes present across every organism in a sample, and targeted amplicon sequencing, which doesn't require an isolate to be generated, are the stars of the show.
"We're looking at everything that's in stool specimens from outbreaks and trying to identify some common genomic material across these samples," Cole explained. By employing these techniques, Cole and her team hope to not only detect known pathogens, but to also look for new and existing pathogens that may have mutated in such a way that makes them difficult to detect using other, more common surveillance methods.
The CDC is currently collaborating with 9 public health laboratories in the U.S. to improve surveillance. "We're really encouraging this to be a collaborative effort between the CDC and public health labs, which is really exciting," Cole said. "We're trying to adapt our protocols (i.e., targeted amplicon sequencing and shotgun metagenomics) to existing protocols in the public health labs to make it so that everything is as similar as possible to things that they're already doing" to integrate new protocols into existing workflows as seamlessly as possible. "[The labs] are pretty excited about it," she added, "which gets me excited, too." Cole also credits the success of this work to the epidemiologists on the team. "We really couldn't do any of this without the epidemiologists finding quality outbreak samples to run our tests," she said.
Cole has donned a variety of hats throughout her career thus far. She attributes finding her current passion in food safety and bioinformatics with having the room to explore new avenues of science as often as possible.
"Don't ever let someone limit you from trying new things. I've done a lot of different types of research, and I've found myself in these different positions, and I've found joy in each of them. Now, I've been able to specialize in something that I really enjoy. I don't think I would have been able to do that if I hadn't tried the different things that came my way," Cole said. "If you'd asked me 6 or 7 years ago if I would be doing bioinformatics, I would have said 'absolutely not.' But I found that it is for me, and I'm having a good time doing it."
