Editor's note: This story was updated on Aug 14 with comments from Robert Britton, PhD.
A large genomic study of the gut bacterium Clostridioides difficile suggests the strains that have become endemic in healthcare systems around the world belong to an emerging species that's genetically adapted to spread among hospital patients.
The research, published in a letter yesterday in Nature Genetics, found that the emerging species of C difficile arose around 76,000 years ago and began to expand around the end of the 16th century, prior to the emergence of the modern healthcare system. Genomic analysis revealed that the ability of the strains in this species to spread in the healthcare system has been aided by genes that help them colonize the gut and produce hardier spores.
C difficile is the leading cause of hospital-acquired diarrhea in the world, but the explosion of cases and emergence of outbreak strains in hospitals has mainly occurred over the past 40 years, and has been linked to rising use of broad-spectrum antibiotics, which wipe out the normal gut bacteria that keep C difficile in check. When that balance is disrupted, C difficile multiplies and produces toxins that cause inflammation of the colon and severe diarrhea.
While antibiotics, and the acquisition of genes that make it more virulent and resistant to certain antibiotics, have played a significant role in making C difficile one of the most common healthcare-associated pathogens, these findings suggest that the genetic adaptations that have occurred over thousands of years set the stage for human, healthcare-related transmission.
Genomic analysis reveals an emerging species
To better understand how C difficile has evolved and what genetic changes have made certain strains more amenable to the healthcare environment, a team led by scientists from the Wellcome Sanger Institute performed whole-genome sequence analysis on 906 C difficile strains isolated from humans, animals, and environmental sources in 33 countries. More than half of the strains came from the United Kingdom, which saw major hospitals outbreaks of C difficile from 2003 to 2007. The collection of strains, which was designed to capture C difficile's genetic diversity, was categorized into four different phylogenetic groups: PG1, PG2, PG3, and PG4.
Analysis of the genetic differences among the strains found that PG1, PG2, and PG3 were all genetically closer to each other than to PG4 and likely descended from that group. The genetic similarities between these three groups indicated they belonged to a similar species, dubbed clade A, while PG4 formed its own species (clade B). The strains in clade A account for 68.5% of the C difficile strains in the US healthcare system, 74% of those found in European hospitals, and 100% of those found in Chinese hospitals.
The analysis also found that one particular strain in clade A—ribotype 027 (RT027), which is one of the major strains implicated in hospital outbreaks—began to expand around 1595 AD.
Further analysis identified the genes that differentiate the two clades and have helped clade A adapt to the modern healthcare environment. These include genes that help make C difficile spores—the dormant forms of bacteria that can survive in inhospitable environments, like hospital surfaces—resistant to hospital disinfectants and therefore more likely to spread from patient to patient. When the researchers exposed spores from both clades to hydrogen peroxide for 5 minutes, the spores from clade A were more resistant than those from clade B.
Other genes the researchers identified in the clade A genomes are involved in the metabolism of fructose and glucose, two simple dietary sugars that are abundant in many of the processed foods that make up a large part of the Western diet.
Theorizing that these genes, when exposed to fructose and glucose, could help C difficile colonize the gut, the researchers tried an experiment with mice. They added fructose or glucose to the drinking water of mice, then infected one group of mice with a clade A strain and another with a clade B strain. Tests of mouse fecal samples indicated a higher bacterial load in the mice infected with the clade A strain.
The researchers also found that when they grew clade A and clade B strains in petri dishes and exposed them to fructose or glucose, the clade A strains produced more spores.
The role of diet
The research builds on another C difficile study published in Nature last year. In a series of mouse experiments, a team of researchers led by Robert Britton, PhD, of Baylor College of Medicine found that two epidemic strains of C difficile—RT027 and RT078, which both belong to clade A—grow better in the presence of trehalose, a sweetening ingredient commonly used in frozen foods like ice cream. They also found that trehalose increases the virulence of RT027.
The researchers noted that the hospital outbreaks of RT027 and RT078 coincided with the widespread adoption of trehalose by food companies after it was approved by the Food and Drug Administration in 2000.
"On the basis of these observations, we propose that the widespread adoption and use of the disaccharide trehalose in the human diet has played a significant role in the emergence of these epidemic and hypervirulent strains," Britton and his colleagues wrote.
Britton told CIDRAP News that the new study "supports the overall premise that C difficile is adapting to the alterations we have made in our diet over the past 200 years." And he suggests that C difficile isn't the only gut bacterium being affected by these alterations.
"It's an exciting area and I would bet that this adaptation is not specific to C difficile but likely also occurs in normal members of the human gut microbiota," he added.
While mouse experiments don't prove that diet has accelerated the rise of C difficile in humans, Nitin Kumar, PhD, a senior bioinformatician at the Wellcome Sanger Institute who co-authored the study, says the findings from these experiments, along with the genomic evidence he and his colleagues documented, suggest that the modern human diet may be playing a role. But research in humans is needed to substantiate that hypothesis.
"Future studies studying the gut microbiome of patients infected with C difficile and how its composition changes with a sugar-rich diet would be useful to understand what is happening in humans," Kumar told CIDRAP News.
And if sugar-rich foods are playing a role, Kumar said, patients with clade A strains might be able to control the infection by adjusting their diet. "This new understanding of C difficile evolution suggests that one way to fight C difficile is to include a low-sugar diet for those patients who are infected with C difficile clade A," he said.
See also:
Aug 12 Nat Genet study
Jan 3, 2018, Nature study on dietary trehalose and C difficile
