Microbiology and Infection for the OR

This is Unit Two of Tech in Surgery Prep. Unit One ended with a scrub person who heard a risk and said it aloud. This unit is about the risk that cannot be heard or seen at all: microbes. Carry one idea through this lecture. In surgery, the question is never whether microbes are present, because they are everywhere. The question is whether they reach a place they should not be. A worked example near the end shows why that question has to be answered at every link, every time. By the end you will be able to tell the main kinds of microbes apart, and say why spores and prions matter. To walk the chain of infection. To define a surgical site infection and say where it comes from. And to apply the precautions, hand hygiene and decontamination levels that break the chain.

Four entries on the microbes themselves, including two forms that survive what kills almost everything else.

They are already here.

TSC 026 Microbes Everywhere

Microorganisms are living things too small to see, present in water, soil, air and on every human body. The commonest are bacteria, viruses and fungi, and many on the body are harmless or helpful. So surgery never asks whether microbes are present; it asks whether they reach a place they should not be.

Three groups, three behaviours.

TSC 027 Bacteria, Viruses and Fungi

Bacteria are single cells. Viruses have no cells of their own and multiply only inside a host's cells. Antibiotics can kill bacteria or stop them multiplying, but do nothing to viruses, and fungi, such as yeasts, are a third group. That is why an antibiotic before surgery targets bacteria and not a viral illness.

A form that survives boiling.

TSC 028 Endospores Survive Boiling

Some bacteria form endospores, dormant forms that survive boiling water and many chemicals. They include the bacteria behind tetanus, gas gangrene and botulism, and a guideline ranks spores as the most resistant microbes apart from prions. So sterilization must be proven to kill spores, and boiling an instrument does not sterilize it.

Not a cell, not a virus.

TSC 029 Prions Are Different

Prions are infectious agents made of an abnormally folded protein, and they cause diseases such as Creutzfeldt-Jakob disease. The national sterilization guideline calls them extremely resistant to ordinary sterilization and disinfection, and says the standard scheme does not solve their inactivation. Suspected cases follow the facility's own instructions.

Six entries on how infection moves: the chain it needs, the flora we all carry, the routes it travels, and the defenses that stop it.

Six links in a chain.

TSC 030 The Chain of Infection

Infection spreads only when all six links are present, and breaking any one stops it. The causative agent, such as a bacterium. The reservoir where it lives, most often the human body. The portal of exit, such as blood or wound drainage. The mode of transmission, such as hands or instruments. The portal of entry, and in surgery the incision is one. And the susceptible host, the patient weakened by illness, age or the operation. Sterilization, hand hygiene, gloves and skin preparation each cut a link. The incision is a portal of entry made on purpose, and sterile technique keeps it from connecting to the rest.

Flora that stays, and flora that washes off.

TSC 031 Resident and Transient Flora

Normal flora live on the body without causing disease, in two groups. Resident flora live deep in the skin and survive ordinary hand hygiene; transient flora are picked up by contact and wash off. Because resident flora return after washing, scrubbed hands still go into sterile gloves.

The skin the incision crosses.

TSC 032 Skin Flora and the Incision

Healthy skin carries its own community of microbes, which helps keep other microbes from settling. Different bacteria dominate moist, dry and oily areas; staphylococci are common in moist places such as the nostrils and armpits. An incision carries those skin microbes toward deeper tissue, so the skin is prepared with an antiseptic first.

Five ways to travel.

TSC 033 How Germs Travel

Microbes reach a new host by five routes. Direct contact, such as hands touching a wound. Indirect contact on an object called a fomite, such as an instrument, a surface or an unchanged glove. Droplets from coughing or talking, which fall within a short distance. Airborne particles that stay suspended, so rooms for airborne diseases use special air handling. And vectors such as mosquitoes and ticks. Most spread in health care is by contact. Indirect contact is the route surgery controls most, because a poorly processed instrument or a contaminated hand can carry microbes into an incision unseen.

Whose defenses are weaker.

TSC 034 Who Is Most at Risk

How likely someone is to develop an infection depends on their defenses. Older age, chronic illnesses such as diabetes, a weakened immune system and poor nutrition all raise the risk. And every surgical patient is a susceptible host to some degree, because the operation itself opens a way in.

The body's own barriers.

TSC 035 The Body's First Defenses

The body's first defenses keep microbes out, flush them away or destroy them. Intact skin keeps them out, mucous membranes trap them, stomach acid destroys many that are swallowed, and cilia sweep mucus from the airways. An incision, a burn or a cut breaks the skin barrier and creates a portal of entry the body did not have.

Five entries on what happens when microbes reach the wound, and on the infections health care itself can cause.

Read inflammation correctly.

TSC 036 Inflammation, Read Correctly

Inflammation is the body's second defense: redness, heat, swelling, pain and loss of function. Damaged cells release chemicals such as histamine, bringing more blood to warm and redden the area while leaking fluid causes swelling. It is protective and part of healing, and does not by itself mean infection; the clinical team judges that.

What counts as a surgical site infection.

TSC 037 Surgical Site Infection Defined

A surgical site infection is an infection in the wound or around the incision within thirty days, or within a year for a deep infection involving an implant. Microbes reach the wound from the patient's own skin, bowel or mucous membranes, or from hands, instruments or the environment. They enter at the portal the operation made, multiply if defenses and prevention fall short, and often show days later, at home. So prevention works early: preventive antibiotics are in the tissue before contamination, and sterile technique, skin preparation and clean instruments limit what arrives. Those who cause an infection rarely see it, so a break is corrected the moment it happens.

From inside, or from outside.

TSC 038 Where Surgical Infections Come From

Contamination of a surgical wound is either endogenous, from the patient's own skin, bowel and mucous membranes, or exogenous, from the team's hands, the air, instruments and supplies. Exogenous sources are the ones the scrub person controls directly through sterile technique, so they are never allowed to slip.

Infections acquired in care.

TSC 039 Health Care–Associated Infections

An infection acquired while receiving care is a health care–associated infection, and surgical site infections are among the most common. Others include bloodstream infections from central lines, urinary infections from catheters, and pneumonia linked to ventilators. The risk grows with longer stays, more invasive procedures and more antibiotic exposure.

When antibiotics stop working.

TSC 040 Resistant Organisms

Multidrug-resistant organisms are bacteria that certain antibiotics no longer control. Examples include methicillin-resistant Staphylococcus aureus, known as MRSA; vancomycin-resistant enterococci, known as VRE; and Clostridioides difficile, which forms spores. They are harder to treat and more dangerous, so preventing spread matters even more.

Seven entries on the practices that break the chain, then two worked examples. The opening idea is paid off at the first of them.

The minimum, for everyone.

TSC 041 Standard Precautions

Standard precautions are the minimum practices for every patient, infection known or not. They treat all blood, body fluids except sweat, broken skin and mucous membranes as possibly infectious. The elements are hand hygiene; protective equipment whenever exposure may occur; respiratory hygiene; cleaning and disinfecting the environment and equipment; safe handling of laundry and waste; sharps safety; and aseptic technique for invasive procedures. In surgery every case qualifies, because blood is expected. A patient with no known infection gets the same protection, because carriers often have no symptoms.

Three added categories.

TSC 042 Contact, Droplet and Airborne

Transmission-based precautions are added for patients known or suspected to carry certain organisms. Contact precautions, for organisms such as MRSA or Clostridioides difficile, add gloves, a gown and dedicated equipment, and for Clostridioides difficile, soap and water, because alcohol rubs do not remove its spores. Droplet precautions, for organisms such as influenza, add a mask and eye protection. Airborne precautions, for measles or tuberculosis, add a fit-tested respirator and a special isolation room. The receiving department is told before a patient on precautions is moved, and in surgery the circulating nurse coordinates the facility's steps.

The single most important practice.

TSC 043 Hand Hygiene Comes First

Hand hygiene is the single most important practice for preventing the spread of infection in health care. An alcohol-based rub is preferred unless hands are visibly soiled or the patient has Clostridioides difficile, when soap and water are used. Gloves do not replace it: hands are cleaned before gloving and after.

Three rising levels.

TSC 044 Cleaning, Disinfecting, Sterilizing

Decontamination rises through three levels. Cleaning removes visible soil; disinfection kills most microbes on objects but not all spores; sterilization destroys all microorganisms, including spores. Every item is cleaned first, because soil left on an instrument can shield microbes from disinfection or sterilization.

Skin chemicals and surface chemicals.

TSC 045 Antiseptics and Disinfectants

Antiseptics are antimicrobial chemicals safe for living skin and tissue, such as povidone-iodine before an incision; disinfectants are stronger and used only on objects and surfaces. Degerming means reducing microbes on skin by scrubbing, as in handwashing. A product ending in cidal kills microbes; one ending in static only stops their growth. Every chemical's effect depends on contact time, the number and kind of microbes, and whether soil is in the way. The wrong chemical in the wrong place harms: a disinfectant can injure skin, and an antiseptic does not make an instrument safe for surgery.

Following one infection back.

TSC 046 Tracing One Infection Backwards

A worked example, constructed for this course, pays off the opening idea. Ten days after a hernia repair, a patient returns with a red, draining incision, and a culture grows a staphylococcus, common on skin. The infection-prevention team works back through the chain: the incision was the portal of entry, and the patient's diabetes weakened defenses. The skin preparation, the preventive antibiotic and the tray's sterilization records were all in order. But the case notes show a torn glove, noticed only minutes later. That is one possible route; the patient's own flora is another. Nobody can prove which. Because an infection rarely traces to one moment, every link is guarded every time.

A patient on contact precautions.

TSC 047 An Isolation Patient Comes to Surgery

A worked example, constructed for this course, follows a patient whose leg wound is colonized by MRSA. The unit nurse calls ahead before transport, and the wound is covered for the trip. The circulating nurse reviews the facility's isolation policy with the team. Standard precautions apply as always. Contact precautions add to them: patient equipment is kept to what is needed, items are not carried in and out during the case, and unsterile staff wear gowns and gloves to touch the patient. The scrub person's field work does not change, because sterile technique already protects the field from every source. Afterwards the room is cleaned under the contact-precaution policy, and anyone unsure what is asked of them asks before the patient arrives.

Look at what you can now do. You can tell bacteria, viruses and fungi apart, and say why spores and prions resist what kills other microbes. You can walk the six links of the chain of infection, and explain flora, the routes microbes travel, who is at risk, and the body's barriers. You can define a surgical site infection, say where its microbes come from, and name the infections health care can cause. And you can apply standard and transmission-based precautions, hand hygiene, and the three levels of decontamination. Unit Three turns to the anatomy the incision crosses.