Clinical: Culture Negative Surgical Site Infections

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Surgical site infections (SSIs) are defined as infections of skin or underlying soft tissues at the surgical site, following an operation. These are common postoperative complications. Nearly 25% of cases develop SSIs, and are more common following emergency surgical procedures. SSIs are associated with tissue destruction up to varying depths, delay or even failure in wound healing, disfiguring or disabling scars, persistent or recurrent pain at the operated site, bacteremia, pyrexia, and incisional hernias. In addition, they also prolong the hospital stay and increase the costs.

This article is an overview of surgical site infections with emphasis on culture negative SSIs. For a detailed review, please refer to the published literature [1] [2] [3]

Management of SSIs is based on a structured protocol, which are as follows:

  • Appropriate preoperative management, which include assessment and optimisation of various risk factors (Table 1).
  • Initiating antibiotic prophylaxis to cover the common pathogens causing SSIs (Table 2).
  • Controlling the operating theater environment and avoiding hypothermia.
  • Appropriate intra-operative management of the tissues and incision.
  • Appropriate postoperative management which include optimisation of hyperglycemia, supplemental oxygenation, judicious use of blood transfusion, nutritional support with emphasis on early enteral nutrition.

The incidence of SSIs can be reduced significantly with these evidence-based protocols [4] [5]. Despite the efforts, 2 to 10% of all elective surgical cases might develop SSI. Further management of such infected wounds is simplified to a certain extent by the culture and sensitivity reports, by being familiar with the hospital microbiological data and by administering nutrition supplements which facilitate wound healing. Such attempts may limit the prolonged hospital stay and will also reduce the costs [6].

Table 1: Risk Factors for the development of SSIs[7]

Patient Factors:

  • Diabetes
  • Malnutrition (undernutrition & obesity)
  • Extremes of age
  • Skin disease at operation site
  • Irradiation at operation site
  • Peripheral vascular disease (for lower limb surgeries)
  • Hypoxemia
  • Postoperative anemia
  • Steroid therapy
  • Chronic inflammatory conditions
  • Infection at remote sites
  • Staphylococcal carriers

Treatment Factors:

  • Emergency procedures
  • Inadequate and inappropriate antibiotic prophylaxis
  • Prolonged preoperative hospitalisation
  • Prolonged operative time
  • Hypothermia
  • Surgical drains

Environmental Factors:

  • Inadequate skin antisepsis
  • Inadequate sterilization of instruments
  • Inadequate ventilation
  • Contaminated medications

Table 2: Microbiology of surgical site infection[8]

Pathogen Incidence (%)
Staphylococcus 19
Coagulase-negative Staphylococcus 14
Enterococcus 12
Escherichia coli 8
Pseudomonas 8
Miscellaneous aerobic gram-negative bacilli 8
Enterobacter sp. 7
Streptococcus 6
Klebsiella sp 4
Miscellaneous anaerobic bacteria 3
Miscellaneous aerobic gram-positive bacteria 2

A common problem is managing a patient with all the clinical signs of surgical site infection, but with “no bacterial growth” on the culture report! The incidence of such ‘culture negative SSIs’, based on published studies can be up to 30%[9] [10]This article will provide an overview of culture negative SSIs. For a detailed review on surgical site infections, please refer to published literature (see references).

Many micro-organisms (Table 3) and non-infective factors (Table 4) are responsible for causing culture negative surgical site infections.

Table 3: Micro-organisms causing Culture Negative SSIs[11]

Common: Atypical mycobacteria Mycobacteria fortuitium Mycobacteria abscessus Mycobacteria chelonae Genital mycoplasmas Mycoplasma hominis Ureaplasma urealyticum Anaerobes

Uncommon: “Small colony variant” Staphylococcus aureus Nocardia Actinomyces Legionella species Coxiella burnetti Gordona species Herpes simplex virus

Organisms incorrectly dismissed as “contaminants” (usually with foreign bodies) Coagulase-negative staphylococci Cornybacteria

Table 4: Non-Infectious causes5

Pyoderma gangrenosum Factitious inoculation

Modes of inoculation of microbes causing culture negative SSIs There are three ways by which microbes gain access to the wounds.

  • Inoculation at the time of surgery is the most common way. This occurs from external sources like contaminated surgical solutions or implants. Examples are rapidly growing mycobacteria (RGM) and Legionella species.
  • Inoculation from patient’s own flora as a result of insufficient antisepsis at surgical site. Examples are Staphylococcus epidermidis and other Coagulase-negative staphylococci, Corynebacterium species (especially during genitourinary tract procedures) and Mycoplasma species.
  • Inoculation during the postoperative period by hematogenous route from a remote site. Mycoplasma can at times gain access to surgical wounds by this infrequent method.

Causes of culture negative SSIs Various causes have been hypothesized for causing culture negative infection at surgical sites:

  • The most frequent cause is thought to be due to culturing the infected site after commencement of antibiotics.
  • Atypical organisms do not grow on standard culture media. Also they may grow rather slowly and the culture plates are discarded before the growth becomes apparent.
  • Common contaminants (like S. epidermidis, Corynebacterium species) are often not given importance, when in fact they may be the actual cause of the infection at surgical site.

Role of microbiologist in detecting SSIs Various media like blood, chocolate, MacConkey agar and anaerobic media are routinely used for detection of the microorganisms. The standard practice is to incubate the culture material (from infected surgical sites) for 3 to 4 days. If no growth is seen, these plates are discarded and the result is reported as ‘no growth’ or ‘culture negative’.

However, certain organisms like RGM grow only after 3-5 days of incubation. Mycoplasmas grow as tiny colonies that may be overlooked. Hence communication with the microbiologist should be a standard clinical practice to ensure optimal identification of the microbes. The laboratory would incubate the cultures for a longer period (5 days or more) and also use special media (Table 5).

Table 5: Duration & Types of Media Used in Identification of Microbes[12]

Medium Incubation Period Microbes Isolated
Sheep blood agar Aerobic for 3 days Staphylococcus aureus & CNS
MacConkey agar Deep tissues: 7 days Streotococci, Enterococci, G-ve rods,Corynebacteria
Choclate agar Aerobic 4 – 7 days Most RGM, Nocardia species

SCV Staphylococcus aureus Occasional: Legionella & Mycoplasma

Buffered charcoal-yeast extract agar (BCYE) Aerobic 4 -14 days Legionella, Mycoplasma & Nocardia, RGM. Fungi, SCV S. aureus
CDC-anaerobic agar, CAN, LKV, Anaerobic 14 – 28 days Anaerobes, Nocardia species,SCV S. aureus, Brucella,
A7 & A8 agar Aerobic 3 – 4 days Mycoplasma, Ureaplasma
Thioglycolate broth (Blood culture bottles) Aerobic 7 – 14 days Growth for all routine microbes, Atypical remain alive for subculture
10B Arginine broth Aerobic 3 – 4days Special broth for recovery of Mycoplasma and Ureaplasma
7h9 broth with PANTA Aerobic up to 14 days Antibiotic supplements broth for recovery of Mycoplasma species
RGM: Rapidly growing mycobacteria. SCV: Small colony variant

Microbes causing culture negative SSI on routine media Pathogenic microorganisms that cause surgical site infections and which do not exhibit growth up to 3 days on routine media are:

  • Atypical Mycobacteria
  • Mycoplasma and Ureaplasma
  • Legionella
  • “Small-colony variant” Staphylococcus aureus
  • Anaerobic pathogens

Atypical Mycobacteria: RGM are a group of atypical mycobacteria. Important species of this group are Mycobacteria abscessus, M. chelonae and M. fortuitum. They take 5 days or more to grow on standard blood agar. SSIs caused by RGMs include:

  • Breast operations
  • Liposuction
  • Spinal surgery
  • Facial surgery
  • Laparoscopy
  • Pacemaker implantation
  • Arthroplasty
  • Minor cutaneous operations
  • Body piercing (especially nipple)

Atypical mycobacteria are susceptible to a wide range of antibiotics, especially fluoroquinolones. Sensitivity of each isolate is recommended.

Mycoplasma and Ureaplasma There are many species of Mycoplasmas. In humans, Mycoplasma hominis and Ureaplasma urealyticum also called as genital mycoplasmas (GM) cause SSIs. Endogenous flora are the likely sources and immunosuppressed patients are more prone. On gram stain, presence of multiple white cells without visible bacteria is predictive of infection with GM. They require special culture methods for optimum identification, as these are not included in routine culture protocols and must be requested by the surgeon. However M. hominis may occasionally appear on standard media as characteristic “fried-egg” pinpoint colonies. SSIs caused by GM include:

  • Cesarean section wounds
  • Sternotomy wounds
  • Vascular grafts
  • Solid organ allograft
  • Orthopedic wounds
  • Maxillofacial wounds
  • Cosmetic surgical sites

GM species are susceptible to tetracyclines and macrolides

Legionella Legionella species are known for causing lung infections, but can also cause SSIs by gaining access to surgical wounds by hematogenous route. They also spread by nosocomial route. They are thin gram-negative bacilli and are poorly visible on gram stain. They do not grow on ordinary culture media and need addition of special substances like cysteine and iron salts for optimal growth. Case reports of SSIs caused by Legionella species include:

  • Hemodialysis fistula
  • Hip surgery wounds
  • Sternotomy wounds

Legionella species are generally susceptible to fluroquinolones or macrolides

“Small-colony variant” Staphylococcus aureus (SCV) These are a form of Staphylococcus aureus. They are not recognised on routine culture media as they grow slowly. They also have a delayed coagulase positive test which can be delayed up to 24 hours. The common (or the wild type) S aureus compared takes just 4 hours to exhibit coagulase positivity. For this reason, these are commonly identified as coagulase-negative staphylococci. The best way to recognise them is to incubate for at least 3 days and look for pinpoint colonies, and then to await the coagulase positive test.

These microbes have a reduced metabolic capacity and are therefore less pathogenic. However, it can persist intracellularly and cause chronic infection, and are resistant to routine antibiotics (which are effective against the wild type). They are very common in patients who have received or are on antibiotics, especially aminoglycosides. SSIs caused by SCV tend to be chronic, like a recurrent draining hernioplasty wound with an implanted mesh. They are generally susceptible to clindamycin and medications that are effective against MRSA.

Anaerobic Bacteria: The surgical site infections caused by these tend to be rare, but can result in a fulminant infection! Common organisms are Clostridium, Bacteroides and Prevotella species. They cannot be cultured on routine aerobic media and need special anaerobic media7. Appearance of dirty-water like exudates, which is culture negative, is a clue to the presence of these bacteria (C. perfringens). Infections caused by such organisms have a high mortality rate and debridement should be done early. They are susceptible to clindamycin and penicillins.

Pathogenic organisms commonly dismissed as contaminants Coagulase-negative staphylococci (CNS) and Corynebacterium species are common pathogens which cause surgical site infections and yet diagnosed as ‘contaminants’! If they are found on repeat cultures or are present in exudates at ~ 105 colony-forming units/ml then they should be diagnosed as the cause of SSI.

Coagulase-negative staphylococci (CNS) Most commonly causes SSI in presence of foreign bodies, prosthetic devices (vascular grafts, shunts, prosthetic joints) and are easy to recognise. CNS can also cause SSIs in the absence of these aforementioned situations. These include complicated and soiled intra-abdominal surgical sites with persistent drainage and already on antibiotics.

Corynebacterium species (“Diphtheroids”) These organisms are common skin commensals and appear in catheter related infections and as blood culture contaminants. However, they can cause infections of implanted devices and unfortunately are dismissed as contaminants! These grow within 3 days and are easily recognised as Corynebacterium species. Various species have been associated with SSIs and hence should not be dismissed as harmless contaminants.

Miscellaneous Pathogens These comprise of a mixture of microorganisms can be difficult to culture and cause SSIs. They are:

  • Nocardia
  • Actinomyces
  • Coxiella burnetti
  • Gordona species
  • Herpes simplex virus type1 (HSV1)

These cause infections at various surgical sites. The case reports include chronic sternal infections and mediastinitis following cardiac surgery, carotid artery rupture following resection of oropharyngeal carcinoma, facial infections following facial-cutaneous surgery. These microbes need special culture media and PCR analysis to diagnose7.

Management of culture negative SSIs Can be described in the following steps:

  • Discuss with the microbiologist and provide all the clinical details, including the antibiotics in use (immediate past and present). The microbiologist in turn needs to do the following:
  • Review the gram stain. This includes original smears as well as stains of broth into which the specimen has been inoculated
  • Review the original culture plate and hold it up to 2 weeks to allow growth of slow-growing’ microbes
  • Can subculture on specialised media
  • Request for a fresh specimen, which should be sent to laboratory immediately, which can then be cultured for acid-fast bacteria and fungus
  • Consider empiric therapy (after vigorous attempts have been made to identify the responsible pathogen in concurrence with the microbiologist) if SSI persists after routine treatment with first-line antibacterial drugs against common pathogens. The choice of antibiotics includes antistaphylococcal penicillins, cephalosporins, vancomycin, and β-lactum / β-lactumase inhibitor combination for suspected mixed infections.
  • Consider additional diagnostic tests and special culture media and repeat cultures.
  • Consider newer fluroquinolones like levofloxacin on long course basis, as these are active against Mycoplasma, Legionella and other atypical mycobacteria.

Conclusion Managing surgical site infections when microbiological diagnosis is not forthcoming is a common and a challenging clinical problem in our surgical practice. In such situations, an effective communication with the microbiologist and infectious-disease specialist will enable a positive outcome. The steps can be summarised as follows:

  • The standard plates to be incubated for an additional 5 to 7 days, which allows the ‘slow-growers’ to be identified.
  • Subculture the broth even in the absence of visible growth
  • Repeat surgical biopsies if diagnosis is doubtful, with a request for special diagnostic studies

Practice Points to Minimise Incidence of Culture Negative SSIs

  • Optimise preoperative morbidity
  • Ensure adequacy of operation theatre environment
  • Ensure adequate antisepsis at surgical sites
  • Ensure appropriate tissue handling
  • Prevent breakdown of infection control procedures

(a)Avoid rinsing instruments in contaminated surgical solutions, tap water or contaminated ‘sterile water’. (b)Avoid contaminated gentian violet marking solutions

  • Institute appropriate evidence-based prophylactic antibiotics


  1. Guidelines for Prevention of Surgical Site Infections. Hospital Infection Control Practices Advisory Committee, January 1999
  2. Shawn S Forbes, Wesley J Stephen, et al. Implementation of evidence-based practices for surgical site infection prophylaxis: Results of a pre- and postintervention study. J Am Coll Surg. Vol. 207, No:3, September 2008
  3. Fry DE. The economic costs of surgical site infections. Surg Infec (Larchmt). 2002; 3 (suppl 1): S37-43.
  4. Guidelines for Prevention of Surgical Site Infections. Hospital Infection Control Practices Advisory Committee, January 1999
  5. Shawn S Forbes, Wesley J Stephen, et al. Implementation of evidence-based practices for surgical site infection prophylaxis: Results of a pre- and postintervention study. J Am Coll Surg. Vol. 207, No:3, September 2008
  6. Fry DE. The economic costs of surgical site infections. Surg Infec (Larchmt). 2002; 3 (suppl 1): S37-43.
  7. Philip S Barie, Soumitra R Eachempati. Surgical Site Infections. Surg Clin N Am. 85 (2005) 1115-1135
  8. Philip S Barie, Soumitra R Eachempati. Surgical Site Infections. Surg Clin N Am. 85 (2005) 1115-1135
  9. Giacometti A, Cirioni O. Epidemiology and microbiology of surgical wound infections. J Clin Microbiol 2000;38:918-922
  10. Twum-Danso K, Grant C, et al. Microbiology of postoperative wound infections: A prospective study of 1770 wounds. J Hosp Infect 1992; 21:29-37
  11. Giacometti A, Cirioni O. Epidemiology and microbiology of surgical wound infections. J Clin Microbiol 2000;38:918-922
  12. Manual of Clinical Microbiology. Washington. D.C. ASM Press, 1999
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