Researchers from Sanford Burnham Prebys have teamed up with prominent drug developer Roche Pharma to learn how bacteria develop antibiotic resistance.

Their new results, published in the journal mBio, are one piece of a long-standing collaboration between the two organizations, the goal of which is to mitigate the growing threat of antibiotic resistance by developing more “irresistible” drugs and by helping improve antibiotic prescribing practices.

“The emergence of antibiotic resistance is inevitable for any single drug, new or old. It’s only a question of time,” says senior author Andrei Osterman, PhD, a professor at Sanford Burnham Prebys. “But the precise time is different for every drug and every microbe, so studying when and how resistance to antibiotics evolves gives us powerful information for improving antibiotic treatment.”

Antibiotic resistance develops rapidly

When a patient is treated with antibiotics, most individual bacteria die, but a few cells will survive, usually as a lucky consequence of a random genetic mutation. These survivors go on to multiply into a whole new population of antibiotic-resistant bacteria.

“The development of antibiotic resistance is a strictly Darwinian process, very similar to evolution in larger organisms,” says Osterman. “The difference is that in bacteria, it happens much more rapidly, which makes antibiotic resistance one of the most pressing challenges facing medicine today.” 

Although the speed at which evolution occurs in bacteria makes antibiotic resistance a threat, the researchers were also able to take advantage of this speed to study its development. The team cultured three species of bacteria in a morbidostat, a device that allows bacteria to grow continuously over multiple generations while being dosed with antibiotics. Although theirs was not the first morbidostat device, the team designed a new, more effective version of the system for their experiments.

“It’s like an evolution machine, letting us watch the development of antibiotic resistance in real time and in an environment that more accurately models what happens to bacteria in a clinical setting than other approaches,” says Osterman. “This gives us a clearer and more comprehensive view of resistance than we’ve ever had before.”

Different bacteria develop resistance differently

By observing the bacteria’s evolution in the morbidostat and sequencing their genomes as they evolved, the researchers found that all three species had a similar pattern of resistance development. However, they also found subtle differences in the ways certain genes were expressed, particularly those that help bacteria remove toxins, a critical process in developing resistance.

“It’s like three remakes of the same movie by three different directors, and their comparison gives us a wealth of information to guide the development and use of antibiotics,” says Osterman. 

Understanding resistance is critical to reducing its harm

Working with Roche, the team has completed similar studies on several other classes of antibiotic drugs, which is helping Roche identify promising candidates for antibiotics that are less prone to resistance.

And because antibiotic resistance is often not assessed in drug candidates until years into the process, using resistance to screen for drug candidates this way could save the biomedical industry millions of dollars and help patients benefit from effective drugs sooner.

“A completely ‘irresistible’ drug is a holy grail, something we can never truly achieve,” says Osterman. “But some drugs are less resistible than others, and our methods allow us to figure out which is which in a systematic way.”

In addition to helping develop new drugs, the researchers claim that their findings are easily translatable to the clinic, where doctors can use detailed knowledge of resistance to select optimal drug combinations with less likelihood of failure due to resistance.

“We are moving away from trial-and-error approaches in medicine and moving toward being able to predict exactly what drugs will work best for each patient,” says Osterman. “It is going to take time, effort and money to make this happen, but it will all be worth it if we’re able to alleviate the threat of antibiotic resistance and help save lives, which I’m confident can be done.”

Deficiencies in vitamins and minerals are a major global health threat, affecting two billion people worldwide. Scientists have extensively studied how human biology is affected by imbalances in vitamins and minerals, also known as micronutrients. But much less is known about the effects of micronutrient deficiencies on gut microbes, which also play important roles in human health and disease.

Sanford Burnham Prebys Medical Discovery (SBP) researchers provided an important contribution to a new study, which addressed this gap in knowledge by comparing the effects of deficiencies in vitamin A, folate, iron, and zinc on gut bacteria in mice. As reported May 17th in Science Translational Medicine, vitamin A deficiency had the largest effect on bacterial community structure and gene activity, increasing the abundance of Bacteroides vulgatus, a species previously associated with host growth.

“The current study provides preclinical evidence supporting the concept that the treatment of micronutrient imbalances needs to be considered from the perspective of not only the human host, but also the host’s gut microbiota,” says study co-author Andrei Osterman, PhD, a professor at SBP.

Hidden hunger

Micronutrients enable the body to produce enzymes, hormones and other molecules essential for proper growth and development. The human body doesn’t need a large amount of these substances, but the consequences of their absence are severe. In particular, imbalances in iron, zinc, folate and vitamin A represent a pressing global public health problem, disproportionately affecting children and pregnant women who live in low-income countries.

To examine the effects of iron, zinc, folate and vitamin A deficiencies on gut microbes, Osterman teamed up with senior study author Jeffrey Gordon, M.D, a professor at Washington University School of Medicine. They first colonized mice with a large and diverse community of human gut bacterial strains. Next, they subjected the mice to a diet oscillation, which began with a micronutrient-sufficient diet, followed by a diet that lacked one of the four micronutrients under investigation, followed by a return to the original diet.

By sequencing microbial RNA and DNA in fecal samples, the researchers examined the effect of diet on the bacterial community structure and gene activity. Surprisingly, they found that vitamin A deficiency had the most profound effect, significantly increasing the abundance of B. vulgatus. Repletion of vitamin A in the diet decreased the abundance of this bacterial species, which has been positively associated with host growth in mouse models of postnatal human gut microbiota development.

Reassessing supplements

Currently, the World Health Organization recommends high-dose vitamin A supplementation for infants and children in high-risk areas, for good reason. Deficiency in vitamin A, which plays important roles in vision, growth, and immune function, is a significant public health problem in more than half of all countries. It is the leading cause of preventable blindness in children and increases the risk of disease and death from severe infections. In pregnant women, vitamin A deficiency causes night blindness and may increase the risk of maternal mortality.

Although adequate levels of vitamin A are crucial for survival, some evidence suggests that micronutrient supplementation can actually cause health problems. The new findings add to these concerns, raising the worrying possibility that vitamin A supplementation might have the unintended consequence of inhibiting the growth of infants and children. But for now, there is not enough evidence to conclude that vitamin A imbalances influence host growth through their effects on B. vulgatus.

“However, our results provide a rationale and a preclinical method for examining whether current vitamin A dosing regimens, and by extension other critical micronutrients, have unintended and deleterious effects on the developing gut microbiota of undernourished children, whose healthy growth such treatments are intended to promote,” Osterman says.