Where standard diagnostic methods see monomicrobial infections, metagenomic methods may recognize polymicrobial infections, such as those recently implicated in necrotizing fasciitis, or flesh-eating disease. What’s more, the metagenomic methods can identify individual members of a polymicrobial infection team. These methods could even reveal the different roles that the individual members play, potentially improving the application of existing therapies. For example, a metagenomic analysis could indicate whether an infection might be best treated with a mixture of antibiotics.
A new study by a team of scientists that included researchers from the University of Maryland and the University of Texas Medical Branch used metagenomic analysis to reveal how two different strains of a single species of flesh-eating bacteria worked in concert to become more dangerous than either one strain alone. The study appeared November 11 in the Proceedings of the National Academy of Sciences, in an article entitled, “T6SS and exotoxin A of flesh-eating Aeromonas hydrophila in peritonitis and necrotizing fasciitis during mono- and polymicrobial infections.”
A patient was infected with four A. hydrophila strains, three clonal (NF2, NF3, and NF4), and one (NF1) phylogenetically distinct,” the article’s authors detailed. “By traditional clinical methods, this case was classified as a monomicrobial infection. Metagenomics analysis revealed polymicrobial infection.
“Clonal strains harbored exotoxin A (ExoA), and NF1 strain possessed a unique effector of the type 6 secretion system (T6SS). The role of T6SS and its effector TseC in direct killing of NF2 in vitro and in vivo and in bacterial phagocytosis/intracellular survival was demonstrated, and the evidence provided that T6SS and ExoA influence dynamics and outcome of mixed infection in NF disease.”
In two previous papers, the scientists isolated and identified two genetically distinct strains of the bacteria that caused necrotizing fasciitis. They labeled those strains necrotizing fasciitis 1 (NF1) and necrotizing fasciitis 2 (NF2). In laboratory studies, neither strain produced a deadly infection on its own. But when the strains were combined, the resulting infection became deadly.
In the current study, the researchers manipulated the genetic components of each strain. When they swapped the genetic components that varied between the strains, the team was able to make NF1 behave more like NF2 and vice versa. By testing the mutant strains in mice, the team determined how the genetic variations affected each strain’s ability to cause infection and interact with the other strain.
“This research provides clear evidence that a very severe infection considered to be caused by a single species of a naturally occurring bacterium actually had two strains,” said Rita Colwell, a distinguished university professor at the University of Maryland Institute for Advanced Computer Studies and a co-author of the study. “One of the strains produces a toxin that breaks down muscle tissue and allows the other strain to migrate into the blood system and infect the organs.”
The three studies combined paint a clear picture of how NF1 and NF2 behave both in separate infections and when combined. In single-strain infections, NF1 remains localized, does not spread to the bloodstream or organs, and is cleared by the host immune system. NF2, however, produces a toxin that breaks down muscle tissue and allows it to spread to the bloodstream or organs.
When the strains occur together, the story is reversed. In multistrain infections, the toxin produced by NF2 breaks down the muscle tissue and enables NF1 to travel to the bloodstream or organs where it becomes deadly. In addition, NF2 remains localized and does not have an opportunity to spread because when it comes into contact with NF1 strains, the NF1 injects a component, an effector delivered by the T6SS contact-dependent secretion system, into NF2 and kills it.
“We’re excited by this very elegant detective work,” Colwell said. “We now have the ability through metagenomics to determine the individual infectious agents involved in polymicrobial infections. With these powerful new methods, we can determine how microbes work together, whether they’re bacteria, viruses, or parasites.”
The ability to identify the agents involved in polymicrobial infections, whether they are different species or variant strains of a single species, can significantly improve treatment outcomes for infected patients.
“When we treat with a given antibiotic, we’re clearing an organism out of the body,” Colwell said. “But if there’s another organism that’s participating in the infection and that’s also pathogenic, then any antibiotic treatment that doesn’t also target that organism may just be clearing ground for it to grow like crazy.”
Treating only one organism in a polymicrobial infection could be the cause of many secondary infections and chronic infections that resist treatment. According to Colwell, a mixture of antibiotics or therapeutic drugs may be necessary to treat polymicrobial infections. Routinely using the metagenomic approach that was developed in this study to analyze infections could result in more effectively targeted treatments for diseases caused by polymicrobial infection.