My condolences for your loss.
Cal. Govt. Code 27520, provides: "(a) The coroner shall perform or cause to be performed an autopsy on a decedent, for which an autopsy has not already been performed, if the surviving spouse requests him to do so in writing. If there is no surviving spouse, the coroner shall perform the autopsy if requested to do so in writing by a surviving child or parent, or if there is no surviving child or parent, by the next of kin of the deceased.
(b) The coroner may perform or cause to be performed an autopsy on a decedent, for which an autopsy has already been performed, if the surviving spouse requests him to do so in writing. If there is no surviving spouse, the coroner may perform the autopsy if requested to do so in writing by a surviving child or parent, or if there is no surviving child or parent, by the next of kin of the deceased. (c) The cost of an autopsy requested pursuant to either subdivision (a) or (b) shall be borne by the person requesting that it be performed."
As you can see from the law, if you request, in writing, that the county coroner perform an autopsy, and you pay for the service, then the coroner must perform the autopsy. The legally operational term used in the above-quoted code section is "shall perform." In law, the term, "shall," means that a duty is mandatory. The coroner does not have the option to refuse the autopsy request, provided that you present it in writing and pay for the cost.
Govt. Code 24971(a) provides a list of causes of death about which the coroner must investigate: "It shall be the duty of the coroner to inquire into and determine the circumstances, manner, and cause of all violent, sudden, or unusual deaths; unattended deaths; deaths where the deceased has not been attended by either a physician or a registered nurse, who is a member of a hospice care interdisciplinary team, as defined by subdivision (e) of Section 1746 of the Health and Safety Code in the 20 days before death; deaths related to or following known or suspected self-induced or criminal abortion; known or suspected homicide, suicide, or accidental poisoning; deaths known or suspected as resulting in whole or in part from or related to accident or injury either old or recent; deaths due to drowning, fire, hanging, gunshot, stabbing, cutting, exposure, starvation, acute alcoholism, drug addiction, strangulation, aspiration, or where the suspected cause of death is sudden infant death syndrome; death in whole or in part occasioned by criminal means; deaths associated with a known or alleged rape or crime against nature; deaths in prison or while under sentence; deaths known or suspected as due to contagious disease and constituting a public hazard; deaths from occupational diseases or occupational hazards; deaths of patients in state mental hospitals serving the mentally disabled and operated by the State Department of State Hospitals; deaths of patients in state hospitals serving the developmentally disabled and operated by the State Department of Developmental Services; deaths under such circumstances as to afford a reasonable ground to suspect that the death was caused by the criminal act of another; and any deaths reported by physicians or other persons having knowledge of death for inquiry by coroner."
It is not clear from your facts, that the coroner must investigate your son's death, because it's not certain that the death was caused by a "contagious" disease (e.g., TB, measles, rabies, etc.). Of course a bacterial infection can be contagious, especially MERS, of the sort associated with hospital and surgical procedures. But, there's some discretion here, because not every bacterial infection is antibiotic resistant. On balance, I believe that the coroner will investigate this death. But, if he/she does not, then you may visit the coroner's office, present a written request for an autopsy, and an offer to pay.
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