The human body is home to millions of commensal microbes, some of which—given the right circumstances—can cause disease. One such microbe, known as nontypeable Haemophilus influenzae (NTHi), infects the lungs of patients with chronic obstructive pulmonary disease (COPD), a condition that makes sufferers more susceptible to long-term, chronic infections.
These pathogenic strains of NTHi may carry unique genetic traits that enable them to persist in COPD lungs. And not all of them make the bug more virulent: Some of these genetic changes actually reduce the microbe’s ability to survive outside the COPD lung, yet improve its odds of survival in diseased tissue, according to a study recently published in mBio.
“The work is exciting because it demonstrates a process that we hypothesized must happen when commensals adapt to unusual disease states,” says University of Pittsburgh microbiologist Vaughn S. Cooper, who was not involved with the study. “It actually shows the consequences of that genetic adaptation for microbial fitness.”
To identify the genetic variations that enable NTHi to adapt to life in the COPD lung, microbiologists Junkal Garmendia of the Public University of Navarra in Spain and Joshua Chang Mell of Drexel University, along with their colleagues, examined the genomes of bacteria isolated from patients’ lungs over a period of one to nine years.
The team collected sputum samples from 13 COPD patients when they visited the hospital for routine checks or during disease flare-ups, and sequenced the genomes of isolated microbes to observe their genetic markers. They then categorized bacteria into groups of isolates that were closely related genetically. Different groups, they found, colonized patients at different points in time. The same group was often re-isolated from the same patient at multiple times or found in different patients. Many groups showed recurrent mutations across several genes.
One of these—a mutation that rendered the fadL gene nonfunctional—appeared in approximately one-third of all the groups. This gene encodes a membrane protein that helps bacteria import long-chain fatty acids, and also binds to a cell surface protein to help the microbe invade human epithelial tissue. The researchers used computational models to test the effects of fadL mutations and found that mutant bacteria would likely lose both these abilities.
But in experimental studies, losing this gene’s functions appeared to be a disadvantage: Mutant bacteria lacking the FadL protein invaded cultured human epithelial cells substantially less than wild-type strains. In a mouse model of lung infections, bacterial numbers for fadL mutants were lower than those of control strains 48 hours after infection.
“This mutation makes the bacteria bad colonizers, so how is it helpful?” asks Mell. “We were confused about how the loss of this gene mattered in chronic infections, so we turned to the protein’s function as a transporter of fatty acids.”
The team compared bacterial growth in minimal media containing fatty acids such as arachidonic acid, which act like detergents and inhibit bacterial growth. Wild-type strains were less viable in the presence of the fatty acid, but fadL mutants were resistant to its antimicrobial effects. “What’s remarkable is the detail with which the work resolves this idea that commensals adapting to new disease states may evolve by losing functions that are costly in other environments but locally beneficial,” Cooper says.
Although the fadL mutation was common in isolates from COPD patients’ lungs, a comparison to publicly available H-flu sequences showed that it’s rare in isolates from other parts of the body— even among pathogenic isolates that cause ear infections or meningitis. “It really impressed us that this mutation was so rare in genomes isolated from other locations,” says Mell, adding that this implies an “important adaptation” allowing the microbe to survive in the COPD lung. “The loss of this gene essentially drives this common commensal to be a pathogen because it can’t grow anywhere else,” Mell says. “There’s a lot to be explored still with how decreasing virulence may actually be a good adaptation for a pathogen.”
“The strategy of capturing in vivo evolution has enormous potential as a tool to learn about key adaptive forces at play during bacterial infections,” adds Carnegie Mellon university microbiologist Luisa Hiller, who was not involved with the work. “We learn about bacterial weaknesses and also about how they adapt to get around the weakness.”