Ballarat parents Brendon Farquhar and Steff Bignold were absolutely delighted when they welcomed their second son, Cooper, safely into the world on December 29.

It followed a difficult pregnancy for Ms Bignold, who ultimately needed to be induced early as she had contracted cholestasis - a liver disease.

The tough pregnancy ended with Ms Bignold hemorrhaging after birth and tiny Cooper having a rough start to life with kidney problems.

After a few days in hospital, his relieved parents were able to take him home and begin their new journey as a family of four.

But just days afterwards, their lives changed.

"Everything was going fine for a couple of days but then we noticed that he was really sleepy and he wouldn't wake to feed," Mr Farquhar said. "He just seemed a bit off."

The behaviour worried the two young parents.

Their first son, Bentley, is almost two-years-old. Described as a "little bundle of absolute joy", Bentley, who has been diagnosed with autism, has taught his parents patience, resilience and how to rise above the daily challenges of being parents of a child on the spectrum. And they wouldn't have it any other way.

While their second child arrived into the world earlier than expected and with some complications, little Cooper's parents were overjoyed as they had both longed to complete their family with a second child.

So when he seemed unwell at just eight-days-old, they had a maternal health nurse visit their house. She identified that Cooper's sleepiness could be due to an underlying problem and recommended that his parents take him to emergency.

His parents immediately followed the advice and within hours, as he was being monitored, little Cooper's condition rapidly declined.

"He stopped breathing on his own and started to seize," Mr Farquhar said. "They inserted a breathing tube and put him on a ventilator to breathe for him as he couldn't do it on his own."

Since that day, these machines have kept little Cooper alive.

With his worsening condition, Cooper was rushed from Ballarat Base Hospital to the the Neonatal Intensive Care Unit (NICU) at the Royal Children's Hospital in Melbourne.

Cooper was transferred in a Paediatric Infant Perinatal Emergency Retrieval (PIPER) ambulance and the terror his shocked parents were feeling escalated.

At the hospital, his tiny body was hooked up to tubes and wires to monitor his vital signs and bodily functions.

Doctors have undertaken countless tests and scans to determine the cause of Cooper's illness since he was admitted to hospital, with his parents by his side as blood has been drawn and spinal taps attempted.

After several anxious days without answers, his parents have since been informed that Cooper has an infection in the fluid around his brain and spine which is affecting his central nervous system.

As it is so rare, with experienced doctors telling the distraught parents that they have only ever seen a handful of cases, it is an extremely emotional time.

Cooper slips in and out of consciousness as he fights for his life.

"It's been a whirlwind of emotions. The shock is starting to wear off now and we are starting to process it a little bit more and think of what's to come rather than just panicking," Mr Farquhar said.

They are taking it day by day and are trying to maintain a positive attitude, with their most immediate hope that Cooper will try to breathe on his own. But even if he is disconnected from the ventilator, he will still be fighting an active infection.

Doctors are continuing to investigate the cause of Cooper's illness, meaning his frightened family is facing the unknown.

"The doctors are trying him on different medications but nothing has worked as of yet," Mr Farquhar said. "[They] said we will be here for a long time and we are not sure what the plan is going to be or what will come next."

Tragically, it is feared that Cooper may have sustained neurological damage though this cannot be determined yet in a baby of such a young age.

Mr Farquhar said staff at the hospital had been fantastic and were helping them to understand what was happening every step of the way.

He urged other parents to trust their instincts and to seek help if they feel something is wrong with their baby as circumstances could change so quickly.

In addition to the challenge of being separated from their son Bentley, who is being cared for by his grandparents in Ballarat as they spend all of their time at the hospital, the pair are beginning to face financial difficulties. At the weekend, Mr Farquhar created a Go Fund Me page.

A move he never anticipated making, he said that he and his partner were not only feeling terrified and hopeless but that the increasingly difficult financial situation was causing extra stress.

With a wish to remain by his son's side, Mr Farquhar cannot return to work to earn his pay cheque.

While they have always tried to be independent, they decided to reach out for financial assistance to ease their financial burden.

Preexisting costs for their mortgage, bills, food and pet food are all normally paid with this income but with mounting costs for hospital parking and petrol, they are struggling.

As of Monday afternoon more than $8000 had been raised, and Mr Farquhar said he and his family were grateful for every cent and message of support.