Sepsis and SIRS: Code It Right in ICD-10-CM

Sepsis and SIRS: Code It Right in ICD-10-CM

Small differences in guidelines can result in major differences in reimbursement.

Sepsis, systemic inflammatory response syndrome (SIRS), and septicemia have historically been difficult to code. Much of the confusion has been due to changing terminology, evolving definitions, and guideline updates over the past 20 years. ICD-10-CM will introduce more changes to sepsis and SIRS coding.

It’s critical to code sepsis properly due to the impact the diagnosis has on reimbursement. For example, consider the following case study:

A 39-year-old patient was admitted with the diagnosis of community-acquired pneumonia in the setting of presumptive influenza and concurrent sepsis. In the history and physical exam, it was documented that the patient had sepsis and SIRS, meeting the criteria of leukocytosis, fever, and tachypnea, with pneumonia as the source. The sputum culture was positive for pseudomonas pneumonia. The patient had a six-day stay. The discharge diagnoses were influenza with pneumonia bacterial superinfection, positive for pseudomonas, as well as acidosis, asthma exacerbation, hypoxemia, and chronic bronchitis.

Sepsis and SIRS were not mentioned on the discharge summary, and are mentioned only sporadically throughout the progress notes. As the documentation stands, the coding is:

Diagnostic Related Group (DRG): 194, $5,694.01

J11.08 Influenza due to unidentified influenza virus with specified pneumonia

J45.901CC Unspecified asthma with (acute) exacerbation [complication and comorbidity]

E87.2CC Acidosis

J15.1 Pneumonia due to Pseudomonas

R09.02 Hypoxemia

J42 Unspecified chronic bronchitis

If you queried the physician regarding whether he or she agreed with the diagnosis of sepsis, and it resulted in a positive response, the chart would be coded:

DRG: 871, $10,621.61

A41.9 Sepsis, unspecified organism







The difference in reimbursement between the two scenarios is $4,927.60 — a significant amount. The documentation of sepsis and SIRS must be solid to code a chart accurately and receive proper payment.

Sepsis progresses in clinical stages. The ICD-9-CM codebook defines these stages in the guidelines; the ICD-10-CM draft does not. To help you understand what is necessary for proper coding, let’s review the stages of sepsis, common documentation issues, coding tips, and coding examples.

Localized Infection

Sepsis almost always begins with localized infection. The source of the systemic infection is typically pneumonia, urinary tract infection (UTI), cellulitis, or a complication of a surgery or device. When these infections are contained, they are self-limiting, but sepsis can occur when the infectious organisms enter the blood stream. For this reason, it’s important that localized infections are identified and treated promptly.

Documentation issues: Often, a patient with a localized infection may exhibit tachycardia, leukocytosis, tachypnea, and fever, but not truly have SIRS or sepsis. These are typical symptoms of any infection. It’s up to the physician’s clinical judgment to decide whether the patient has sepsis or SIRS. You cannot assume the patient has sepsis or SIRS based on the criteria being met — you must rely on the physician’s documentation.

Coding tips: Per the guidelines, if the patient is admitted with a localized infection and sepsis or severe sepsis, the code for the systemic infection should be assigned first, followed by a code for the localized infection. If the patient is admitted with a localized infection and the patient does not develop sepsis or severe sepsis until after the admission, the localized infection is coded first, followed by the appropriate codes for sepsis or severe sepsis.

Example: A patient is admitted with pneumonia and acute hypoxic respiratory failure. On day four, the patient worsens and becomes hypotensive and is diagnosed with sepsis, septic shock, and acute renal failure. On the discharge summary, pneumonia is documented as the principal diagnosis.

J18.9 Pneumonia, unspecified organism

J96.01 Acute respiratory failure with hypoxia

A41.9 Sepsis, unspecified organism

N17.9 Acute kidney failure, unspecified

R65.21 Severe sepsis with septic shock


Bacteremia is a lab finding of infectious organisms in the blood. The patient has no clinical signs of sepsis or SIRS. Bacteremia may be transient, or may lead to sepsis. When a patient’s blood cultures are positive and not believed to be a contaminant, the patient is usually treated with antibiotics.

Documentation issues: The coding of bacteremia is not based on blood culture results (whether negative or positive), but on the physician’s documentation of the condition. If the patient has bacteremia with sepsis, the alphabetic index directs you to “see sepsis.” When both bacteremia and sepsis are documented, code only sepsis. If different physicians document bacteremia and sepsis, and the documentation conflicts, query the attending physician.

Coding tips: According to AHA Coding Clinic™, second quarter 2011, if bacteremia is associated with a local infection, the local infection is coded first, followed by the bacteremia, and then the infectious organism.

Example: A 79-year-old patient is admitted with dizziness and fever. A urine sample is collected on admission and is positive for Klebsiella. The blood sample taken on admission is also positive for Klebsiella. The doctor lists: UTI due to Klebsiella, bacteremia due to Klebsiella.

N39.0 Urinary tract infection, site not specified

R78.81 Bacteremia

B96.1 Klebsiella pneumoniae [K. pneumoniae], as the cause of diseases classified elsewhere


Septicemia is a systemic disease associated with the presence and persistence of pathogenic micro-organisms or their toxins in the blood. Whereas the patient with bacteremia was not symptomatic, the infectious organisms of septicemia cause symptoms. This is not a transient lab finding: The condition warrants inpatient admission with antibiotics and supportive treatment.

Documentation issues: Septicemia is rarely a term physicians document, and to reflect this shift in terminology, the term “septicemia” in ICD-10-CM’s alphabetic index refers you to “sepsis.” Various causative organisms and septic conditions are listed under the entry.

Example: A 39-year-old woman is admitted with high fever, malaise, and myalgias. Blood cultures and urine cultures taken on admission are positive for E. coli. The patient is diagnosed with septicemia and UTI due to E. coli.

A41.51 Sepsis due to Escherichia coli [E. coli]



SIRS is the body’s clinical cascading response to infection or trauma that triggers an acute inflammatory reaction and progresses to coagulation of the blood, impaired fibrinolysis, and organ failure. SIRS is manifested by two or more of the following symptoms: fever, tachycardia, tachypnea, leukocytosis, or leukopenia.

Documentation issues: When SIRS is documented on the chart, determine if it’s due to an infectious or non-infectious cause. SIRS due to a localized infection can no longer be coded as sepsis in
ICD-10-CM. If “SIRS due to pneumonia” is documented, the
term “sepsis” must also be documented to code a systemic infection. This is a major change from ICD-9-CM. If the term “sepsis” is not documented with “SIRS” when it’s due to a localized infection, you must ask for clarification from the physician.

Coding tips: In the alphabetic index under “Syndrome, systemic inflammatory response,” you are led only to the non-infectious SIRS (R65.10 Systemic inflammatory response syndrome (SIRS) of non-infectious origin without acute organ dysfunction and R65.11 Systemic inflammatory response syndrome (SIRS) of non-infectious origin with acute organ dysfunction). The guidelines in chapter 1 no longer make reference to SIRS with sepsis and severe sepsis. Guidelines pertaining to SIRS are now found in chapter 18.

Non-infectious causes are the result of trauma, burns, pancreatitis, drug reaction, etc. When SIRS is due to a non-infectious cause, the non-infectious process is coded first, followed by R65.10 — or, if organ dysfunction is present, R65.11.

SIRS Criteria Table

Temperature > 38° C or < 36° C (> 100.4° or < 96.8° F)

Heart rate > 90 beats/min

Respiratory rate > 20 breaths/min

WBC > 12,000 cell/mm3 or < 4,000 cells/mm3

Example: A 27-year-old patient is admitted with fever, tachypnea, and a high lipase level. The patient is diagnosed with SIRS due to pancreatitis.

K85.9 Acute pancreatitis, unspecified



Sepsis is a systemic inflammatory response due to an infection. It’s not necessary for blood cultures to be positive to code sepsis.

Documentation issues: You can code for sepsis when the physician documents the term “sepsis.” Documentation should be consistent throughout the chart. Occasionally, during an extended length of stay, sepsis may resolve quickly and the discharging doctor may not include the diagnosis of sepsis on the discharge summary. In these cases, it may be appropriate to ask the physician whether he or she agrees if the patient had sepsis.

When the patient has clinical evidence of sepsis, a negative or inconclusive blood culture does not preclude or rule out sepsis. When the patient has clinical indicators for sepsis, question the provider, even when blood cultures are negative.

Coding tips: In ICD-10-CM, only one code is needed to report sepsis without organ dysfunction. Most sepsis codes can be found in A40.- through A41.9. If the physician specifies a causal organism, such as “sepsis due to E. Coli,” “sepsis with blood cultures positive for E. Coli,” or “E. Coli sepsis,” use the code for sepsis naming the specific organism.

The category A40.- through A41.9 is for sepsis due to bacteria or unspecified bacteria. Fungi, candida, or viruses also may cause sepsis. It’s important to use the alphabetic index to select the appropriate code for the systemic infection. For example, if a patient is diagnosed with candidal sepsis due to a candida UTI, report B37.7 Candidal sepsis as the principal diagnosis and B37.49 Other urogenital candidiasis as the secondary diagnosis. A code from A40.- through A41.9 is not selected because candida is not a bacterial infection.

Example: A 45-year-old woman presents with severe stomachache, fever, vomiting, and bloating. On a computed tomography (CT) scan, a perforated bowel with abscess is discovered. The patient has sepsis with peritoneal abscess as the source. The peritoneal fluid and blood cultures are positive for enterococcus (group D strep).

A41.81 Sepsis due to enterococcus

K65.1 Peritoneal abscess

K63.1 Perforation of intestine (nontraumatic)

Severe Sepsis

Severe sepsis is sepsis with acute organ dysfunction or multi-organ dysfunction. The organ dysfunctions commonly associated with severe sepsis are listed under R65.- Symptoms and signs specifically associated with systemic inflammation and infection in ICD-10-CM.

Documentation issues: If the doctor documents severe sepsis, sepsis with evidence of organ dysfunction, or severe sepsis with elevated lactate but does not specifically name the organ dysfunction, do not code severe sepsis. It’s appropriate to query the physician regarding which organ dysfunction occurred during the admission. You should be able to identify the clinical signs and symptoms of organ dysfunction, and ask the physician about organ dysfunction if it’s not documented.

Occasionally organ dysfunctions such as acute renal failure or acute respiratory failure are documented, but may not be documented as “due to” the sepsis; in which case, severe sepsis cannot be coded. For instance, if severe sepsis, pneumonia, and acute renal failure due to dehydration are documented, the code for severe sepsis may not be assigned because the acute renal failure is not stated as due to or associated with sepsis. If the documentation is unclear, query the physician.

“Multi-organ dysfunction” is not coded. The patient may have many concurrent organ dysfunctions, but they must be specifically named to code them.

Coding tips: When severe sepsis is documented, there will be a minimum of two codes when using ICD-10-CM: a code for the underlying systemic infection, followed by a code for Severe sepsis, R65.2-. If organ dysfunction other than septic shock is present, the codes for the specific organ dysfunction are added.

Note that under R65.2, “Systemic inflammatory response syndrome due to infectious process with acute organ dysfunction” is also listed as an inclusion term. This, however, cannot be indexed under “syndrome, systemic inflammatory response,” and clarification regarding this entry will be necessary.

Example: A 90-year-old patient is admitted with sepsis meeting criteria with tachypnea and tachycardia. The source is determined to be aspiration pneumonia. The patient develops acute hypoxic respiratory failure and acute renal failure related to the sepsis.

A41.9 Sepsis, unspecified organism

R65.20 Severe sepsis without septic shock

J69.0 Pneumonitis due to inhalation of food and vomit

J96.01 Acute respiratory failure with hypoxia


Septic Shock

Septic shock generally refers to circulatory failure associated with severe sepsis, u sually manifested by hypotension. Septic shock is a form of organ failure.

Documentation issues: The term “septic shock” is occasionally documented without the term “sepsis.” According to the guidelines, for all cases of septic shock the code for the underlying systemic infection is sequenced first, followed by R65.21 Severe sepsis with septic shock or T81.12- Postprocedural septic shock. Additional codes for other acute organ dysfunctions should be coded, as well. The code for septic shock can never be assigned as principal diagnosis.

Coding tips: Septic shock does not have a separate code in
ICD-10-CM, as it does in ICD-9-CM. Septic shock is combined into code R65.21.

Example: A patient is admitted with cellulitis and abscess of the left leg, severe sepsis, septic shock, and acute renal failure and encephalopathy due to the sepsis.



L03.116 Cellulitis of left lower limb

L02.416 Cutaneous abscess of left lower limb


G93.41 Metabolic encephalopathy

Post-procedural Sepsis and
Sepsis Due to a Device, Implant, or Graft

A systemic infection can occur as a complication of a procedure or due to a device, implant, or graft. This includes systemic infections due to wound infection, infusions, transfusions, therapeutic injections, implanted devices, and transplants.

Documentation issues: The physician must document the relationship between the infection and the procedure. If the documentation isn’t clear, query the physician. An example of when clarification is necessary is if “sepsis due to complicated UTI” is documented on it. In this statement, it’s unclear as to what is complicating the UTI: could be the patient’s medical condition or it could be an indwelling Foley catheter. The cause of sepsis must be accurately captured because when a complication code is sequenced first, the case will no longer fall into a sepsis Medicare Severity-Diagnostic Related Group and reimbursement will be affected.

Coding tips: When sepsis is due to a complication of a procedure, the complication code will be sequenced first, followed by the code for the specific infection. If the patient has severe sepsis, add R65.2- with the codes for specific organ dysfunctions. If the specific causative organism is known, the code for the infectious agent can be added.

Obstetrical Sepsis

When sepsis and septic shock are complicating abortion, pregnancy, childbirth, and the puerperium, the obstetrical code is sequenced first, followed by a code for the specific type of infection. If the patient has severe sepsis, add R65.2- with the codes for specific organ dysfunctions. If the specific causative organism is known, add the code for the infectious agent. According to the guidelines for puerperal sepsis, a code from category A41 Other sepsis should not be added.

Newborn Sepsis

When a newborn is diagnosed with sepsis, assign a code from category P36 Bacterial sepsis of newborn. If the sepsis isn’t documented as congenital or community acquired, the default is congenital; assign a code from P36. Codes from category P36 include the organism; an additional code for the infectious organism is not assigned. If the P36 code does not describe the specific organism, an additional code for the organism can be assigned.


The term “urosepsis” is not coded in ICD-10-CM. When urosepsis is documented, you must query the physician.

Sepsis Syndrome

Sepsis syndrome also cannot be coded in
ICD-10-CM. You must query the physician when the term “sepsis syndrome” is documented as a final diagnosis.

Know when to Query

Sepsis is a complicated condition to code, and it is often necessary to query the physician to code the case correctly. The guidelines for sepsis refer to querying five times, demonstrating the complexity of these cases and the need to ask for clarification. Query the physician:

  • When the documentation is conflicting, imprecise, incomplete, illegible, ambiguous, or inconsistent.
  • When clinical indicators are present without a definitive diagnosis.
  • When diagnostic evaluation or treatment was performed without a related diagnosis.
  • When a diagnosis is given without clinical validation.
  • When the term “urosepsis” is used.
  • When the term “sepsis syndrome” is used.
  • When severe sepsis is documented without specific organ dysfunctions named.
  • When organ dysfunctions are not documented as due to sepsis.
  • When it is unclear whether sepsis was present on admission.
  • When it is unclear if sepsis is related to a device or to the local infection.

Remember: The current version of ICD-10-CM is a draft. Revisions may still be made when it’s implemented on October 1. Small differences in the guidelines have the potential to result in major changes in principal diagnosis selection and reimbursement.
A careful comparison of ICD-9-CM and ICD-10-CM is necessary to correctly code in the new system.

Jill Kulanko, RHIA, CPC, CIC, COC, CPC-I, CCS, is an educator for her company My Coding Mentor, where she teaches AAPC PMCC curriculum and a variety of other coding-related courses. She is also the owner of Advanced Coding Solutions, Inc., where she has worked as an independent contract coder in the Denver Metro area for more than 20 years in both inpatient and outpatient facility coding. Kulanko is a member of the Denver, Colo., local chapter.

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7 Responses to “Sepsis and SIRS: Code It Right in ICD-10-CM”

  1. Robin says:

    What would be your pdf if the dx is Severe Sepsis secondary to viral enteritis?

  2. Rajesh Kumar K says:

    Excellent Explanation

  3. Debra says:

    A41 codes are secondary only allowed and can be use only with one of the codes listed under the category. It is equivalent to the ICD-9 codes for sepsis due to no infections conditions such as trauma. Sepsis is not the infection it is the response to the infection caused by the presence of an organism. The guidelines state to code first the infection. The infection is not the sepsis it is the UTI or whatever the documented infection is, then you need a causal organism and we are instructed to code this as A41.9 if no other organism is documented.

  4. Mia says:

    Great read. What would be the principal diagnosis if the admitting diagnosis is acute respiratory failure with hypoxia due to a drug overdose, ordered BIPAP, sepsis due to aspiration pneumonia all present on admission?
    Started on IV antibiotics.

  5. ASaiz says:

    Thank you for your comment. You’ll find a lot of suggestions and better answers to your question in the Member Forums.

  6. Jennifer says:

    Per 2017 CDI Pocket Guide by Richard D. Pinson, MD, FACP, CCS, on page 155 when a patient has sepsis and organ dysfunction, a relationship can be assumed and no query is needed to code severe sepsis. Can you please clarify if you agree with this, as this may be a new rule since your last post in 2016. Thanks

  7. Connie says:

    Question? A patient was admitted with sepsis due to a number of diagnoses, uti and the uti was due to the indwelling catherter, pneumonia, sacral decubitus and osteomyelitis. Would the principle dx be complication of a cath/UTI or would it be sepsis?

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