A prisoner who died of a very rare form of meningitis had a 5cm-wide abscess in his skull caused by a fungal infection that was only found after his death.

At first it was thought Boyd Cuttance died from a series of strokes, but on post-mortem an infection with aspergillus fungus was found.

The 44-year-old, who had been a gardener at a plant nursery, was transferred from the Otago Correctional Facility to Dunedin Hospital in January 2012, coroner David Crerar says in a report published today.

He was sentenced and imprisoned in November 2011 for setting fire to cars in the carpark of a Waihola bar and assaulting the bar manager.

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In 2010 he had started getting headaches, which progressed the following year to anxiety, sleepiness, sweating and vomiting. A hospital CT scan in October 2011 revealed an infected sinus and he was put on antibiotics.

In the 48 days after starting his prison sentence, he suffered ills including headaches, neck pain, unconsciousness, dizzy spells and numbness of the lips and a forearm. He was seen by prison nurses and doctors 30 times and the prison's contracted GP three times.

His mother, Elizabeth Cuttance, an enrolled nurse, visited on January 15, 2012 and insisted he be taken to hospital, which was carried out later that day.

In hospital, Cuttance had MRI and CT scans, lumbar punctures - and tests for bacteria and the fungus aspergillus, but nothing showed up. A biopsy of his small intestine diagnosed coeliac disease and he was put on a gluten-free diet.

Pathologist Professor Han-Seung Yoon said in the report of Cuttance's post-mortem that there was a 4-5cm abscess in the subarachnoid space - one of the layers over the brain. The base of an artery was buried in the abscess and was severely narrowed. There was evidence of extensive recent infarcts - areas of dead tissue resulting from loss of blood flow - and many threads of fungi in the abscess.

Neurologist Dr John Mottershead, answering the coroner's questions on cause of death, said the brain tissue showed features consistent with abscess due to invasive infection with aspergillus.

"Dr Mottershead said CNS [central nervous system] infection with aspergillosis is unusual in immune competent people. Possible factors that may have made Mr Cuttance susceptible to this infection include the coeliac disease and his excessive alcohol intake."

Dr Mottershead said: "Although earlier identification of the meningitis or earlier initiation of anti-fungal medication may have altered the outcome, treatment of such infections is not always successful. The possibility of a fungal infection was considered at the beginning of his hospital stay but as seen ultimately in the case, despite advice from experts in microbiology and infectious diseases, it was not possible to isolate a causative organism until post-mortem."

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Cuttance's type of meningitis was very rare and its cause even more rare, Dr Mottershead said.

Cuttance's GP said the October 2011 headaches were probably the start of the sinus disease that developed into the fungal infection of the subarachnoid space. Such fungal infections were "known to have an association with Boyd's type of work as a gardener at a plant nursery. He would have been exposed to fungal spores for compost and rotting vegetable matter. It is often associated with an immune compromised patient or poorly controlled diabetes. To my knowledge this was not the case for Boyd".

Mr Crerar criticised the prison over how long it took to send Cuttance to hospital, saying that "30 presentations in a period of 48 days" should have alerted the nurses to the seriousness of the underlying illness, although he also acknowledged the illness was of obscure cause and it was only speculation whether the outcome would have been any different for the prisoner had he been sent to hospital earlier.

The Department of Corrections said thorough assessments were conducted by the prison doctor on December 20, 2011 and January 6, 2012 and blood tests in this time were within the normal range. An investigation by the inspector of prisons found Cuttance's prison health care had complied with Corrections' written policy on health services.