Disinfection and Sterilisation

Every reusable medical device that touches a patient carries a risk of transmitting infection to the next patient, and reprocessing is what removes that risk. The discipline rests on a single organising idea, worked out by Earle Spaulding more than half a century ago: the level of treatment an item needs is set by what that item touches, not by what it is. An instrument that will enter the bloodstream must be rid of all microbial life, while a blood pressure cuff that touches only intact skin needs far less.

This article follows that logic from the classification itself through the chemical and physical processes that achieve each level, then to the two problems that most concern the virologist: reprocessing the flexible endoscopes responsible for more device transmitted outbreaks than any other instrument, and decontaminating the prions that defeat routine sterilisation.

Key definitions

The vocabulary of reprocessing is precise, and the distinctions carry real consequences. Sterilisation is the complete destruction of all microbial life, including bacterial spores, and it is an absolute term rather than a relative one. It is achieved physically by steam under pressure or dry heat, or chemically by ethylene oxide gas, hydrogen peroxide gas plasma, vaporised hydrogen peroxide, or prolonged immersion in a liquid chemical sterilant.

Disinfection eliminates many or all pathogenic microorganisms on inanimate objects with the exception of bacterial spores, and it is usually done with liquid chemicals or wet pasteurisation. The dividing line between disinfection and sterilisation is therefore sporicidal activity: a few liquid chemicals kill spores given several hours of contact, at which point they qualify as chemical sterilants.

Cleaning is the physical removal of visible organic and inorganic soil, and it is the indispensable first step, because residual soil shields microorganisms from every process that follows. Decontamination renders an object safe to handle, while antisepsis applies a germicide to living tissue. The word antiseptic is reserved for skin and mucous membranes; disinfectant is reserved for inanimate objects, even when the active chemical is the same.

The Spaulding classification

Spaulding divided all patient-care items into three categories according to the infection risk they pose, and each category maps to a required minimum level of reprocessing. The scheme has proved durable enough to underpin national guidance worldwide.

Category	What it touches	Infection risk	Minimum reprocessing	Examples
Critical	Sterile tissue or the vascular system	High	Sterilisation	Surgical instruments, cardiac and urinary catheters, implants, arthroscopes and laparoscopes
Semi-critical	Mucous membranes or non-intact skin	Intermediate	High-level disinfection	Flexible endoscopes, laryngoscope blades, respiratory and anaesthesia equipment, endocavitary probes
Non-critical	Intact skin only	Low	Low-level or intermediate-level disinfection	Blood pressure cuffs, bedpans, bed rails, patient furniture, floors

Critical items carry the highest risk and must be sterile, so they are bought sterile or steam-sterilised where possible; heat-sensitive critical items are processed by ethylene oxide, hydrogen peroxide gas plasma or vapour, or a liquid chemical sterilant. Semi-critical items require at least high-level disinfection and are then rinsed, ideally with sterile water, because rinsing with tap water can recontaminate a disinfected endoscope with waterborne organisms such as non-tuberculous mycobacteria or Pseudomonas. Non-critical items rarely transmit infection directly, but their surfaces can act as an intermediary for hands, and they are decontaminated in place with an environmental disinfectant.

Levels of disinfection

Disinfection is graded into three levels defined by the range of organisms killed. High-level disinfection destroys all microorganisms except large numbers of bacterial spores, and the regulatory benchmark is a kill of at least six orders of magnitude of a test Mycobacterium within the labelled contact time, which for the common agents runs from about 12 to 45 minutes at 20 °C or above.

Intermediate-level disinfection kills mycobacteria, vegetative bacteria, most viruses and most fungi but cannot be relied on for spores. Low-level disinfection kills most vegetative bacteria, some fungi and some viruses within about ten minutes, and is the level used for non-critical surfaces. The mycobacterium sits at the demanding end of this scale because its waxy wall resists chemical attack, which is why tuberculocidal activity became the historical proxy for a robust disinfectant.

Cleaning: the essential first step

No disinfection or sterilisation process can be trusted on a dirty instrument. Cleaning removes the organic and inorganic soil that both physically shields microorganisms and chemically inactivates many germicides, and the sequence of cleaning followed by high-level disinfection can reduce a mycobacterial load by more than eight orders of magnitude, with cleaning alone contributing roughly half of that.

Soil that is allowed to dry and bake onto an instrument becomes far harder to remove, so soiled instruments are kept moist until they can be cleaned. Biofilm, the adherent community that builds up inside the narrow channels of endoscopes, is particularly resistant and is a recurring reason for reprocessing failure.

Sterilisation methods

Steam sterilisation is the most widely used and the most dependable method, because it is non-toxic, inexpensive, rapidly sporicidal and penetrates fabrics and lumens well, and it is the least affected by organic soil. It works at two temperatures: 121 °C and 132 °C, with minimum exposures of about 30 minutes at 121 °C in a gravity-displacement steriliser or roughly 4 minutes at 132 °C in a prevacuum steriliser that first pumps air out of the load. Its spore-forming biological indicator is Geobacillus stearothermophilus.

Steam cannot be used for heat-sensitive or moisture-sensitive devices, which is where the low temperature methods earn their place.

Ethylene oxide is a highly penetrating gas that sterilises occluded lumens and heat-sensitive materials at 37 °C to 63 °C over a cycle of one to six hours. Its great drawback is safety: it is flammable, explosive and a known human carcinogen, so a lengthy aeration phase is needed to drive off residual gas before an item is safe to use, which makes each cycle slow.

Despite tightening emissions regulation, which retired the older gas blends in favour of pure ethylene oxide, it remains the only validated method for tens of thousands of heat-sensitive devices, so no ready alternative has displaced it.

Hydrogen peroxide gas plasma excites hydrogen peroxide vapour into a reactive plasma of free radicals at under 50 °C in a cycle of roughly 30 to 50 minutes with no aeration and no toxic residue, but it cannot process cellulose materials such as paper or linen, or liquids, and it has lumen-length restrictions.

Vaporised hydrogen peroxide is similar, leaving only water vapour and oxygen, but it too cannot sterilise the long narrow channels of gastrointestinal endoscopes and bronchoscopes. A newer combination of hydrogen peroxide with ozone overcomes that limit and is cleared to sterilise multichannel flexible endoscopes, part of a wider move to sterilise rather than merely disinfect these devices.

Dry heat remains a recognised sterilising agent for materials that steam cannot penetrate, such as powders and anhydrous oils. Pasteurisation in hot water above 70 °C for 30 minutes is not sterilisation, because it spares spores, but it is an accepted alternative to chemical high-level disinfection for respiratory and anaesthesia equipment.

Chemical disinfectants

The liquid chemicals used for high-level disinfection and for surface decontamination differ markedly in spectrum, speed and toxicity, and choosing between them is a matter of matching the agent to the item and to the compatibility of its materials.

Agent	Usual level	Virucidal spectrum	Key limitation
Glutaraldehyde (≥2%, alkaline)	High-level, sterilant	Broad, including non-enveloped viruses	Fixes blood and tissue to surfaces; respiratory irritant; slow against mycobacteria
Ortho-phthalaldehyde (0.55%)	High-level	Broad	Stains proteins and skin grey; contraindicated for urological instruments
Hydrogen peroxide (improved, 2% or more)	High-level	Broad	Limited activity against Clostridioides difficile spores
Peracetic acid (~0.2% in reprocessors)	Sterilant	Broad and rapid	Corrodes some metals; immersible instruments only
Hypochlorite (chlorine)	Intermediate to high	Broad, including non-enveloped viruses	Corrodes metals, inactivated by organic matter, releases chlorine gas with acid or ammonia
Alcohol (60 to 90%)	Intermediate	Enveloped and many non-enveloped viruses	Not sporicidal; evaporates before achieving long contact
Phenolics	Intermediate to low	Moderate	Contraindicated in neonatal units
Quaternary ammonium compounds	Low	Enveloped viruses only	Not active against non-enveloped viruses, mycobacteria or spores

Glutaraldehyde at 2% or more, buffered to pH 7.5 to 8.5, is a long-standing high-level disinfectant that is cheap and kind to materials and stays active in the presence of organic matter, but it coagulates blood and fixes tissue to surfaces, irritates the airway, and can cause colitis or corneal damage if an instrument is inadequately rinsed.

Ortho-phthalaldehyde acts faster, particularly against mycobacteria, and needs no activation, but it stains skin and proteins grey and is contraindicated for cystoscopes because of anaphylactic reactions reported in bladder-cancer patients.

Hypochlorite is fast, cheap, broadly virucidal and the agent of choice for blood spills, used at a 1:10 dilution of household bleach for large spills and 1:100 for small ones, and at around 5000 parts per million for C. difficile spores.

The quaternary ammonium compounds used to wipe down surfaces are the important cautionary case for virologists: they inactivate enveloped viruses but not the small non-enveloped viruses, so a surface disinfectant chosen for convenience may leave norovirus or an enterovirus untouched.

Reprocessing flexible endoscopes

Contaminated endoscopes have caused more healthcare-associated outbreaks than any other medical device. A flexible gastrointestinal endoscope or bronchoscope is a semi-critical item with long, narrow, valved internal channels that trap organic soil and are almost impossible to inspect, so reprocessing must be meticulous and is a frequent point of failure.

After a leak test, the device is cleaned by brushing and flushing every channel with an enzymatic detergent, then high-level disinfected by immersing it and perfusing the disinfectant through all channels for the labelled time, then rinsed, then dried by flushing the channels with alcohol and forced air, and finally hung vertically to store.

The drying and hanging steps matter as much as the disinfection, because residual moisture in a coiled endoscope lets any surviving waterborne organisms multiply during storage. Peracetic-acid automated endoscope reprocessors, running dilute peracetic acid at around 50 °C, mechanise the disinfection and rinsing steps and reduce operator variability.

Persistent outbreaks have driven a rethink of this whole approach. More than twenty-five outbreaks of multidrug-resistant organisms have been traced to contaminated duodenoscopes, several occurring despite correct cleaning and high-level disinfection, because the movable elevator at the tip is almost impossible to clean reliably. High-level disinfection also leaves no margin of safety: it targets a six-log reduction, whereas sterilisation validates to a one-in-a-million sterility assurance level.

The response has been a shift from high-level disinfection towards sterilisation for the highest-risk flexible endoscopes. Reasoning from Spaulding’s own definition, a duodenoscope that reaches the biliary tree through the duodenum effectively enters sterile tissue and so meets the criterion for a critical item. Regulators moved the same way for urological endoscopes: after reprocessing failures, flexible cystoscopes and ureteroscopes covered by a 2022 field safety notice are now to be sterilised after each use. Single-use designs and terminal packaging that keeps a device sterile until it is opened belong to the same direction of travel.

Environmental surfaces and healthcare waste

The near-patient environment is a genuine reservoir. Surfaces contaminated by one patient can transmit organisms to the next room occupant, and terminal cleaning is frequently incomplete, with audits showing that only about half of high-touch surfaces are actually cleaned.

Routine practice is an environmental-surface disinfectant applied for at least one minute to the high-touch sites nearest the patient, such as bed rails, the bed surface and the overbed table. No-touch technologies, chiefly ultraviolet-C devices and hydrogen peroxide vapour systems, supplement but do not replace manual cleaning, and are reserved for terminal decontamination of rooms that housed patients with persistent pathogens. Surfaces that stay continuously active for many hours after a single application are an emerging addition.

Two current pathogens shape practice. Candida auris, a multidrug-resistant yeast that persists on surfaces and resists some routine disinfectants, calls for a product effective against Clostridioides difficile spores in its rooms. For severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), by contrast, the environment often carries viral genetic material but rarely viable virus, and the fomite route is thought to play only a limited part, so an ordinary hospital disinfectant from the regulator’s emerging-viral-pathogen list, applied to high-touch surfaces, is enough.

Healthcare waste that can transmit infection is segregated at the point of generation and treated before disposal, usually by steam sterilisation or incineration. The most hazardous category includes cultures and stocks of infectious agents and, at the extreme, waste contaminated with the agents of viral haemorrhagic fever such as Ebola, Marburg and Lassa viruses, which is handled under the strictest containment.

Inactivating viruses: from enveloped viruses to prions

Viruses are not equally hard to kill, and the practical determinant is the lipid envelope. Enveloped viruses, including human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are the least resistant of all viruses, because the envelope is easily disrupted by alcohols, hypochlorite and even the quaternary ammonium compounds. The small non-enveloped viruses, such as norovirus, poliovirus and adenovirus, have no such vulnerability and are correspondingly harder to inactivate, which is why they are used as the reference viruses in disinfectant efficacy testing.

For bloodborne enveloped viruses in a spill, a hospital disinfectant labelled effective against HIV and HBV, or diluted hypochlorite, is sufficient; no special procedure beyond standard high-level disinfection and sterilisation is required for the great majority of viral pathogens.

Prions are the single exception that defeats routine sterilisation. The agents of Creutzfeldt-Jakob disease and the other transmissible spongiform encephalopathies are misfolded proteins with no nucleic acid, and they resist the temperatures, chemicals and radiation that inactivate every conventional pathogen.

Special reprocessing is triggered by a specific combination: critical or semi-critical instruments that have contacted high-risk tissue, meaning brain, spinal cord or eye, from a patient with known or suspected prion disease. Such an instrument is kept moist until reprocessing, because drying lets the protein bond to stainless steel, and is then decontaminated by one of several accepted regimens.

These combine sodium hydroxide with autoclaving, for example immersion in 1N sodium hydroxide for one hour followed by autoclaving, or extended steam sterilisation alone at 134 °C for 18 minutes in a prevacuum steriliser or 132 °C for one hour by gravity displacement. Notably, the temperature should not be pushed above 134 °C, because effectiveness can paradoxically decline at higher temperatures. Instruments too delicate or intricate to clean adequately are discarded rather than reused, and disposable instruments are preferred for high-risk neurological procedures.

South African context

South African practice follows the same Spaulding logic and international methods described above, within a local regulatory framework. Disinfectants and detergents are regulated as a distinct class of substance under the Foodstuffs, Cosmetics and Disinfectants Act (Act 54 of 1972), while broader chemical and radiation hazards fall under the Hazardous Substances Act (Act 15 of 1973), and a facility’s infection prevention and control programme is expected to work within both.

Healthcare risk waste is governed by the South African National Standard SANS 10248 and by the Health Care Waste Management Regulations made under the National Health Act, which together set out how a facility identifies, segregates, colour-codes, stores, transports and treats this waste. Infectious waste is rendered safe by incineration or by alternative non-burn technologies such as autoclaving, before final disposal at a licensed facility.

In the public sector, sterile services for reusable instruments are centralised in a hospital’s central sterile services department, where steam sterilisation remains the workhorse and low-temperature methods handle the heat-sensitive minority. Suspected viral haemorrhagic fever imposes the most stringent local requirements for disinfection and waste, which are set out for South African facilities in the South African VHF Guidelines.

References and recommended reading

• Rutala WA, Weber DJ. Disinfection, Sterilization, and Hospital Waste. In: Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases, 10th edition. Elsevier; 2025. The primary source for the classification, methods, agents and the endoscope-sterilisation shift described here.
• South African Bureau of Standards. SANS 10248-1: Management of Healthcare Waste, Part 1: Management of Healthcare Risk Waste from a Healthcare Facility. Pretoria: SABS; 2008. The national standard for healthcare risk waste segregation, treatment and disposal.
• National Department of Health, South Africa. Regulations Relating to Health Care Waste Management in Health Establishments. National Health Act, 2003 (Act No. 61 of 2003). The legislative basis for infectious-waste handling, treatment and disposal in South African facilities.