The alliance of surgery, microbiology, and microbiota in the fight against surgical site infections

Introduction

A surgical wound is any disruption of tissue continuity resulting from a surgical procedure. Its proper healing depends on many factors, primarily on the condition of the surgical site before the procedure. Classifying wounds by the degree of their contamination plays a significant role in surgical treatment, and helps evaluate the risk of developing surgical site infections (SSIs; Table 1). The existence and composition of the microbiota in the region of the body undergoing surgical intervention should also be considered. Therefore, this study aimed to present the problem of SSIs in a microbiological context, with particular emphasis on the role of the microbiota of selected human body niches in the development or prevention of SSIs.

Table 1. Wound contamination classification^1,25,31,32

Surgical wound classification	Description	Typical wound microorganisms (examples)
Clean	Surgical wounds in which there is no inflammation, and the respiratory, digestive, genital, or urinary tracts are not affected. Furthermore, clean wounds are initially closed and, if necessary, drained using closed drainage. This category includes postoperative wounds resulting from nonpenetrating trauma.	Staphylococcus aureus (MSSA/MRSA), coagulase-negative staphylococci (eg, S. epidermidis), Cutibacterium acnes
Clean-contaminated	Surgical wounds in which access to the respiratory tract, gastrointestinal tract, genital organs, or uninfected urinary tract is achieved under controlled conditions and without unusual contamination. This category includes, in particular, wounds associated with surgeries involving the biliary tract, appendix, vagina, and oropharynx, provided there are no signs of infection or significant errors in surgical technique.	Microbiota of the respiratory, gastrointestinal, and urogenital tract: Streptococcus spp., Enterococcus spp., Escherichia coli, and Actinomyces spp.
Contaminated	Open, fresh, accidental wounds; also those associated with operations during which a serious error in surgical technique related to maintaining sterility or significant leakage from the gastrointestinal tract occurred, as well as wounds with acute, nonpurulent inflammation.	Bacteria belonging to the order Enterobacterales (E. coli, Klebsiella spp., Enterobacter spp., Proteus spp.); anaerobes (bacteria from the Bacteroides, Prevotella, Fusobacterium genera); Pseudomonas spp., Acinetobacter spp.
Dirty or infected	Old traumatic wounds with retained necrotic tissue and those that include an existing clinical infection or visceral perforation. This definition suggests that microorganisms causing postoperative infection were present in the surgical field before surgery.	Mixed microbiota: S. aureus (including MRSA), Streptococcus pyogenes, bacteria belonging to the order Enterobacterales, P. aeruginosa, Acinetobacter spp., anaerobes, fungi (Candida spp.)
Abbreviations: MSSA, methicillin-sensitive Staphylococcus aureus; MRSA, methicillin-resistant Staphylococcus aureus

Definitions and epidemiology of surgical site infections

Every patient undergoing surgery is at a risk of complications, including SSIs. The primary pathophysiology of this infection is the entry of microorganisms into the human body through an incision. According to the European Centre for Disease Prevention and Control (ECDC), SSI is defined as an infection involving the incision or operative field that occurs within 30 days after surgery, or within 90 days if an implant is placed, and may involve the skin, soft tissues, deep tissues, or organs / spaces manipulated during the procedure.¹ Due to the importance of this complication and the need to implement appropriate preventive measures, including monitoring the number of infections in each surgical ward, SSIs have been divided into 3 types, and precise criteria have been developed to identify each type (Table 2). In Europe, SSIs are registered under the auspices of the ECDC, as part of the Healthcare-Associated Infection Surveillance Network (HAI-Net).

Table 2. Case definitions of surgical site infections¹

Type of SSI	Description	Criteria for diagnosis
Superficial incisional SSI	Involving only the skin and subcutaneous tissue of the incision	At least 1 of the following: Purulent drainage from the superficial incision (with or without laboratory confirmation); Organisms isolated from an aseptically obtained culture of fluid or tissue from the superficial incision; Presence of at least 1 sign of infection (pain or tenderness, local swelling, redness, or fever) requiring a surgeon to deliberately open the superficial incision unless the incision culture is negative; Diagnosis of superficial incisional SSI made by a surgeon or attending physician
Deep incisional SSI	Involving the deep soft tissue (eg, fascia, muscle)	At least 1 of the following: Purulent drainage from the deep incision but not from the organ / space component of the surgical site; Organisms isolated from an aseptically obtained culture of fluid or tissue from the deep incision (eg, fascia, muscle); Spontaneous wound dehiscence or a need to deliberately open the deep incision due to the presence of infection signs or symptoms (fever >38 °C, localized pain or tenderness) unless the incision is culture-negative; Abscess or other evidence of infection involving the deep incision found on direct examination, during reoperation, or on histopathologic or radiologic examination; Diagnosis of deep incisional SSI made by a surgeon or attending physician
Organ / space SSI	Involving any anatomical part (organs or spaces) other than the incision that was opened or manipulated during surgery	At least 1 of the following: Purulent drainage from a drain that is placed through a stab wound into the organ / space; Organisms isolated from an aseptically obtained culture of fluid or tissue in the organ / space; Abscess or other evidence of infection involving the organ / space found on direct examination, during reoperation, or on histopathologic or radiologic examination; Diagnosis of organ / space SSI made by a surgeon or attending physician
Abbreviations: SSI, surgical site infection

According to estimates, SSIs are one of the most common clinical forms of health care–associated infections (HAIs) in the world. A meta-analysis of 43 studies from 39 countries (data up to 2022) showed a global SSI prevalence of 2.5% (95% CI, 1.6%–3.7%).² An ECDC report published in 2024 stated that SSIs accounted for 16.1% of a total of 22 806 HAIs reported in the European Union / European Economic Area (EU/EEA) in the years 2022 and 2023, and were the most frequent type of HAI on admission (25.7% of total HAIs on admission).³ Detailed data based on 662 309 surgical procedures from 11 EU member states and a single EEA country, from 2021 and 2022, indicate that the percentage of SSIs varied from 0.6% in laminectomies to 9.6% in open colon surgeries. The incidence density of in-hospital SSIs per 1000 postoperative patient-days varied from 0.1 to 5.3, depending on the type of surgical procedure.⁴

Two Polish studies, with data derived from the database of the National Health Fund (NHF), presented the results of observations carried out in the period 2012–2018 in selected orthopedic departments (including the SSI incidence in hip- and knee- arthroplasty procedures), and reported an SSI rate of 0.9%–1.5%.^5,6 In caesarean sections, the average SSI incidence was 0.5%, and significant differences were noted among hospitals (0.1%–1.8%). In the cases where antibiotic prophylaxis was not used, the incidence was 3.1%.⁷

Microbiota of selected body sites and its role in surgical site infection development

Skin

Typically, SSIs are caused by pathogens originating from the patient’s endogenous microbiota, and the most important source is the skin. This organ is an effective barrier against the external environment, and serves as a habitat for microbiota (primarily bacteria, but also fungi, viruses, eukaryotes, and archaea). The composition of the skin microbiome varies depending on the colonization site, which is influenced by temperature, humidity, exposure to sunlight, and access to an oxygen atmosphere (Figure 1).

Microbiota–host interactions promote skin and immune response homeostasis.⁸ Compromising the skin tissue during the surgical incision allows microorganisms to penetrate the wound and disrupt this balance. The risk of developing an infection and its severity are influenced by the body area being operated on and the degree of wound contamination, which determine the presence and abundance of specific microorganisms (Table 1). The duration of the procedure and persistent inflammation postsurgery are also important factors. Disinfectants applied to the skin at the surgical site to remove the microbiota do work, but studies on chlorhexidine gluconate (CHG), among other agents, showed that this approach does not ensure complete efficiency. Furthermore, some patients harbor bacteria that are highly resistant to antiseptics used for preoperative prophylaxis, which is usually due to inappropriate use of these agents.⁹ During disinfection, the skin microbiota is significantly reduced, resulting in lower abundance of commensal bacteria from the Corynebacterium spp., Micrococcus spp., and coagulase-negative staphylococci. These bacteria, through cooperation with other microorganisms, prevent the excessive multiplication of pathogens (eg, interaction with Corynebacterium acnes reduces the virulence of Staphylococcus aureus, S. epidermidis, Escherichia coli, and Candida albicans).⁹ Thus, their decrease may lead to impaired skin microbiome defense against opportunistic pathogens, particularly gram-negative bacteria and other microorganisms found in biofilms. This may be a reason why pathogens such as S. aureus, S. epidermidis, E. coli, and Pseudomonas aeruginosa frequently cause SSIs.^10,11 Studies on various antiseptics (alcohol, povidone-iodine, CHG) indicate that exposure to these agents causes a rapid but short-term reduction in the diversity and abundance of skin microbiota, which likely begins to regenerate within a few hours. Sources of this renewal include areas adjacent to the disinfected area (eg, microorganisms residing deep within the hair follicles), as well as patient’s clothing and home and hospital environments.¹²

Microorganisms present in wounds can also delay healing processes. Selected mechanisms behind this phenomenon are briefly presented in Table 3.

Table 3. Key microbiological mechanisms that delay wound healing^{25,28,31,32,39}

Mechanism	Description
Production of enzymes and toxins (protease, collagenase, homolysis)	It leads to the breakdown of the extracellular matrix and tissue destruction.
Mixed aerobic–anaerobic infections	It causes increased tissue degradation, resulting in poorer drug penetration and local hypoxia.
Opportunistic and drug-resistant bacteria (Pseudomonas spp., Acinetobacter spp., MRSA)	They cause difficult-to-treat chronic infections, directly inhibiting repair processes.
Biofilm	Most chronic, nonhealing wounds contain a bacterial biofilm; the biofilm protects bacteria from antibiotics and the immune system, leading to persistent inflammation and inhibition of the proliferative phase of healing.
Abbreviations: see Table 1

Intestines

Abdominal surgery deserves particular attention, as, in addition to the skin microbiota, the gastrointestinal microbiota may also be involved in the development of SSIs. This ecological niche of the human body is believed to be the richest in microorganisms, with bacteria being the best-studied group. Thanks to the use of modern molecular methods, including next-generation sequencing, we know that the number and diversity of bacteria increase progressively in the lower parts of the gastrointestinal tract, reaching their highest abundance and richness in the large intestine.^13,14 The gastrointestinal microbiota consists primarily of gram-negative bacteria and anaerobes. The variation in microbial numbers according to the gastrointestinal tract region is presented in Figure 2, and the composition of the microbiota in individual gastrointestinal sections is shown in Figure 3.

Disruption of the intestinal walls leads to the migration of microorganisms from the lumen of the digestive tract into the peritoneal cavity, and further into the bloodstream. However, it appears that a breach of the intestinal barrier is not necessary for the development of SSI. The “Trojan horse hypothesis” attempts to explain the link between the intestinal microbiome and infections occurring at distant surgical sites (eg, joint replacement prosthesis infections or infected pancreatic necrosis). This mechanism of metastatic SSIs relies on the action of neutrophils, which “clean” the environment at the borders of the intestinal mucosa, ingest bacteria, and migrate with them into the bloodstream, and then to tissues damaged elsewhere. Bacteria contained within the neutrophil phagosome evade the host defense mechanisms.^15,16

Female genital tract

Dysbiosis of the gut microbiota can also predispose to various pregnancy complications, posing a significant health risk to both the mother and the newborn. Modern research methods have enabled the detection of bacteria in the placenta. Latest studies show that the composition of this microbiota resembles that of the oral cavity and even the intestines, but the placental microbiota exhibits niche specificity. For over a decade, evidence has been emerging suggesting the presence of microorganisms in the uterus.^17-19 The composition of a healthy endometrial microbiota is not entirely known. Still, studies suggest that Lactobacillus and Flavobacterium are the most abundant bacterial genera, showing similarities with the vaginal microbiota profile. Therefore, it appears that vaginally derived bacteria primarily colonize the uterine cavity via the ascending route.¹⁷ Figure 4 presents a profile of the female genital tract microbiota.

Considering the abovementioned reports and the established knowledge on the vaginal microbiota,^13,14,18,20 it is important to understand how the female genital tract microbiota may be a source of surgical complications, such as SSIs following a cesarean section. In the latest Centers for Disease Control and Prevention document presenting the definitions and procedures for the surveillance of SSIs within the US National Healthcare Safety Network, endometritis following a caesarean delivery was classified as an organ / space SSI, and the uterus was considered the primary site.²¹

Management of surgical site infections

SSIs are associated with prolonged hospitalization and poor patient prognosis, contributing to increased mortality and health care costs. Therefore, they constitute a serious public health problem and continue to require special attention and modern methods of diagnosis, treatment, and, above all, prevention.²¹ The risk of developing SSI is associated with many factors, such as the patient’s general condition and factors related to the patient’s environment and treatment organization, as presented in Table 4. Strong predictors of SSI development include an American Society of Anaesthesiology score 3 or greater (severe general condition), an extended surgery duration (>2 h or >75th percentile; this index is used to determine the cutoff point between short- and long-duration surgeries), and presence of a contaminated or dirty / infected wound (Table 1).²²

Table 4. Risk factors of surgical site infections^1,2,25,26

Risk factors	Examples
Patient-related factors	Diabetes (especially uncontrolled glycemia) Obesity (BMI >30 kg/m2) Nutritional deficiencies, hypoalbuminemia Renal failure, dialysis Immunosuppression (steroid therapy, chemotherapy, HIV infection) Chronic diseases of the heart, lung, or liver Extreme age (infants, elderly) Smoking, alcohol use disorder Colonization with resistant microorganisms (eg, MRSA, ESBL)
Surgery-related factors	Degree of wound cleanliness Surgery duration >75th percentile High-risk surgeries (intestinal, gynecological, orthopedic with implants, cardiac) Excessive tissue trauma, necrosis, hematoma Presence of implants, foreign bodies, and drains Inadequate hemostasis Repeated procedures, reoperations Significant blood loss, transfusions Intraoperative hypothermia
Factors related to the medical environment / care protocol	Incorrect antibiotic prophylaxis (poor drug selection, delayed initiation, duration >24 h) Lack of aseptic technique and hand hygiene measures Inappropriate skin preparation (lack of CHG / alcohol disinfection) Lack of perioperative glycemic control Failure to maintain normothermia Improper instrument sterilization High operating room occupancy, time pressure Lack of systematic SSI monitoring and auditing (including after discharge)
Abbreviations: BMI, body mass index; CHG, chlorhexidine gluconate; ESBL, extended-spectrum β-lactamases; others, see Tables 1 and 2

Diagnostics

Crucial elements in managing SSIs are the appropriate microbiological diagnostics of infection and collaboration with a microbiology laboratory. They ensure effective action aimed at rapid identification of the causative or infectious agent and enable the initiation of appropriate treatment. This is important because we are currently grappling with a rapid increase in the number of bacterial strains that are establishing and developing resistance mechanisms to multiple antibiotics.²³

The diagnosis of SSI is based primarily on clinical symptoms (Table 2) and microbiological examination (Gram stain, culture / serology / biochemical / genetic methods, and antibiotic susceptibility testing) of the material collected from infected sites (wound swab, sample of synthetic material, eg, surgical mesh, implant, or necrotic tissue). Certain rules need to be followed: 1) if the patient’s condition allows, the sample should be collected before treatment initiation; 2) if the patient is already receiving treatment, relevant information (medication name, time and route of administration) needs to be provided on the laboratory referral, especially in the case of antibiotic treatment; 3) if the patient is receiving immunosuppressive therapy (eg, chemotherapy), testing for fungal and Mycobacterium tuberculosis infection should be considered; 4) the swab has to be taken from deep within the wound, not from the skin surrounding it; 5) samples need to be sent to the microbiology laboratory as soon as possible; 6) if systemic signs of infection are present, a blood sample for microbiological testing (culture) should be collected.^10,24-26

Treatment

Despite increasing knowledge about the causes and mechanisms of wound formation and the implementation of infection prevention strategies, treatment of infected wounds still poses a significant challenge due to the prevalence of microbial colonization, which leads to biofilm formation, delayed healing, and drug resistance. The primary step in the treatment of most SSIs is debridement, which involves opening the wound, removal of sutures / staples, incision and drainage, and removal of necrotic tissue. Antibiotics should be considered if systemic signs of infection (fever, tachycardia, leucocytosis) or deep / organ space infection are present.^27,28 In such cases, the following approach is recommended: 1) for infections developing after “clean” skin / soft tissue surgery (trunk / head / neck / extremities), an antibiotic active against S. aureus (eg, cephalexin if the strain is methicillin-sensitive, and linezolid or dalbavancin if it is methicillin-resistant) should be initiated; 2) for wounds localized in the groin, gastrointestinal tract, perineum, or gynecological areas (where mixed microbiota is likely to be involved in the infection), an antibiotic active against gram-negative and anaerobic bacteria (eg, cephalosporin with metronidazole, fluoroquinolone with metronidazole, or a combination of an antibiotic with a β-lactamase inhibitor: ceftolozane / tazobactam, ceftazidime / avibactam) should be considered.^27,29

Of note, this is an empirical therapy that should be immediately modified upon receiving microbiological test results (ie, de-escalation of antibiotic therapy to a specific pathogen). The duration of antibiotic therapy is debated, but most guidelines agree that the shorter the duration, the better (assuming a good response and complete control of the source of infection).^27-29

The problem of increasing antibiotic resistance and the formation of biofilm by microorganisms—a structure much more resistant to external factors, such as antibiotics and disinfectants, than the bacteria themselves—forces researchers to seek other therapeutic options. Therefore, increasing emphasis is being placed on strategies combining surgical debridement with the local application of “antibiofilm” agents (eg, nanoparticles of silver, gold, or other semiprecious metals, antimicrobial peptides, bacteriophages and phage enzymes, or intelligent hydrogels that release antibiotics upon stimulation) and additional systemic antibiotic therapy.^28,30-32

Prevention

Many factors influence the course of surgery and increase the patient’s risk of developing SSIs. Reducing the risk of these infections is therefore complex and requires simultaneous implementation of a range of preventive measures before, during, and after surgery. However, their implementation is not uniform worldwide; currently, there are no international guidelines, and recommendations vary by country. Nevertheless, certain principles remain consistent and form the basis for combating SSIs.³³ Because the risk of SSIs depends on many factors (Table 4), various interventions aimed at preventing infections are often combined into a “bundle.” The concept of a care bundle was developed to streamline critical care processes and improve patient outcomes, and is used in various medical fields, including surgery,^11,29,33-36 where it comprises the following steps: 1) patient preparation (including normalization of blood glucose levels, proper nutrition, treatment of comorbidities, S. aureus eradication by using mupirocin nasal ointment and a CHG shower gel in patients undergoing cardiac, orthopedic, and neurological procedures); 2) surgical site preparation (skin cleansing with alcohol-based antiseptic solutions and CHG; hair should not be shaved but rather removed with a clipper, if necessary); 3) surgical hand preparation (scrubbing with appropriate antibacterial soap and water or using an appropriate alcohol-based hand sanitizer before putting on sterile gloves); 4) antibiotic prophylaxis at a single intravenous dose (recommended for patients undergoing “clean” surgery involving the implantation of a prosthesis or implant; “clean-contaminated” and “contaminated” surgery [Table 1]), preferably administered within 60 minutes of the surgical incision; a second dose of antibiotics is most often recommended if the procedure lasts longer than 4 hours; cefazolin is the drug of choice, but in the case of allergies, alternative options, such as clindamycin or metronidazole, are advised; 5) intraoperative measures (maintaining normal body temperature, intensive perioperative glucose level control, maintaining adequate blood volume control, using sterile, disposable, nonwoven or sterile, reusable fabric drapes and gowns, using proper surgical technique and hygienic instrument handling); 6) postoperative measures (proper wound care, not using any advanced dressings covering standard dressings on initially closed surgical wounds, not extending antibiotic prophylaxis after the completion of surgery, wound inspection).

Surveillance is a key element in preventing SSIs. In March 2025, the ECDC published its latest document standardizing the definition and reporting procedures for SSIs in European hospitals.¹ Based on this document, SSIs are recorded in the HAI-Net, which provides a framework for national and regional surveillance systems, including uniform definitions, data collection methods, and reporting standards. As part of the HAI-Net program, a Point Prevalence Survey (PPS) is conducted periodically in all ECDC member countries to assess the point prevalence of HAIs (including SSIs) and antibiotic use. Unfortunately, in Poland, this monitoring system has limitations, as only cases with active infection on the day of the survey are recorded, which underestimates the true number of HAIs (especially those developing after hospital discharge). Furthermore, taking part in the program is voluntary, so not all surgical departments in Poland participate. The PPS is highly useful for cross-country comparisons and rapid assessment of the HAI burden, but it does not replace prospective surveillance of HAIs, including SSIs. Therefore, the ECDC HAI-Net system utilizes 2 parallel tools: PPS and cohort surveillance. The former offers a “bird’s eye view,” while the latter provides precise data on selected surgical procedures.

It is worth emphasizing that the current surveillance system in Poland relies, among other elements, on the continuous detection, classification, and registration of HAIs, most often conducted by a nurse epidemiologist.³⁷ The collected data are analyzed by the Infection Control Team, which includes a physician (serving as the team leader), a nurse specialized in infection epidemiology and control, and a laboratory diagnostician specialized in microbiology. This team also plays a key role in SSI surveillance, working closely with surgeons and other members of the medical staff by: 1) establishing guidelines for perioperative antibiotic prophylaxis (eg, timing, type, and dosage of antibiotics); 2) implementing antiseptic procedures for surgical sites; 3) monitoring compliance with antiseptic techniques in the operating room; and 4) assessing and reporting SSI cases (data are analyzed and presented to surgical department staff, facilitating discussion, education, and procedural adjustments).^37,38

In Poland, the definitions and time criteria for SSIs are identical to the standards outlined in the ECDC document; surveillance is carried out primarily in hospitals, and aggregated data are transferred to the National Institute of Public Health – National Institute of Hygiene (NIH). One of the tasks performed by the NIH is to conduct voluntary surveillance programs for HAIs, including SSIs; however, the data obtained do not cover the entire country and are primarily epidemiological and scientific in nature. The NHF conducts mandatory reporting of medical services and certain complications, but without the detailed classification of SSIs described in the ECDC protocol. For this reason, Polish data on SSIs submitted to the ECDC only originate from hospitals participating in voluntary surveillance projects conducted by the NIH, not from the entire country.^37,38

Conclusions

Given the serious medical, legal, and economic consequences of SSIs, as well as the spread of multidrug resistance among microorganisms, it is crucial to understand the role of the microbiota of various human body niches, especially the skin and gastrointestinal tract, in the development and prevention of these infections. The search for new methods to combat bacterial biofilm and a modern approach to the prevention of HAIs seem essential. There is also a need to improve the surveillance system for HAIs, including SSIs, in Poland, which would contribute to more effective control of these infections.