She has returned to school, is studying for A-levels, has started a part-time job and is learning to drive.
"I think it will pave the way for other such studies to help with getting the necessary trials carried out on bacteriophages so that they can be used more widely to treat humans", he said.
They are the microbial embodiment of the adage: "My enemy's enemy is my friend".
They tested individual phages known to infect bacterial relatives of the patients' strains, and mixed thousands of other phages together and tested the lot.
The experts believe that using more than one strain could help prevent the bacteria from mutating and becoming resistant to the bacteriophage, as they are being challenged by multiple phages at once. Spencer chose to take a gamble on what seemed like a far-fetched idea: phages, viruses that can destroy bacteria and have a long-if checkered-history as medical treatments. "They not only infect, but kill efficiently", Hatfull says.
Isabelle Carnell-Holdaway was born with cystic fibrosis.
Within weeks, the infection began to recede and her condition began to improve.
Isabelle has cystic fibrosis, a genetic disease that results in frequent infections clogging up the lungs with mucus. "My heart sinks when I see that a [lung transplant] patient has got a wound infection, because I know what the trajectory is going to be", says Spencer, Isabelle's respiratory pediatrician at Great Ormond Street Hospital in London.
"For some patients, that's within a year despite aggressive treatment". But her infection persisted after the transplant, threatening her life. However, she has made significant strides in her recovery and now lives a near-normal life.
Doctors said there was nothing they could do, and that Isabelle had a less than 1% chance of survival.
Mrs Carnell-Holdaway told BBC News: 'When we left hospital, she literally looked like a skeleton with skin on, she was so poorly.
Where did the experimental therapy come from?
A breakthrough: Her consultant at Great Ormond Street Hospital in London worked with a team at the University of Pittsburgh to develop an untested phage therapy.
Professor Graham Hatfull, a microbiologist at the University of Pittsburgh was sent samples of Isabelle's infection along with samples of another infected patient. The team genetically modified these phages to maximize their ability to identify and kill this bacteria before combining them into a treatment cocktail for Isabelle.
The place had become an worldwide repository for phages through a program Hatfull had helped develop in which college students around the world isolate and identify phages, learning about biology while expanding knowledge about these viruses that thrive by the trillions within and around us.
Spencer said that "a big lesion" by Isabelle's liver "disappeared, and then we've seen the wounds on the skin just gradually - gradually - just slowly start to heal".
"For them to be able to just have a little fiddle around with these phages and to be able to make them cure something that is a huge global problem is just absolutely incredible", she says. They also note that her tailor-made cocktail doesn't work against other M. abscessus isolates they have tested.
In June 2018, doctors administered the cocktail to the patient via an IV twice daily with a billion phage particles in every dose. Worse still not even the most robust antibiotics were making an impact, and the two teenagers were placed in palliative care. "We are optimistic that in time it can completely clear the infection", Spencer says.
Dr Spencer told BBC News: "It's fantastic really, but also tinged with sadness when I think of all the patients that did not survive as the treatment was not available in time for them". However, a large-scale roll out is unlikely to happen soon, as the treatment is still in the experimental stages and will need refinement, as well as large clinical trials, to prove that it is safe and effective. But a string of recent successes against antibiotic-resistant bacteria have revived interest in the idea, leading major US universities to launch phage research centers.
Phage therapy dates back a century, but until recently the idea was relegated to fringe medicine in most countries, mainly because of the advent of antibiotics.
Viruses and bacteria are the culprits behind the infectious diseases that plague humans.
But now phage-therapy is having a resurgence due to the rise of superbugs that are resistant to antibiotics.
Professor Hatfull called antibiotics "blunt instruments" and said, "With phages it's the opposite end of the spectrum". He identified one that appeared to be good at killing the bacterium, Mycobacterium abscessus, which was causing the girl's infection. If a phage could do that, the team reasoned, it might able to fight the patients' infections.
After the transplant, this fear became a reality: a bacterial strain similar to TB took hold, colonising her surgical wound, then her liver, until eventually pockets of bacteria known as nodules began pushing through the skin on her arms, legs and buttocks.