Sepsis Coding: How to Properly Code Sepsis
Introduction:
Sepsis is a potentially life-threatening complication of an infection and occurs when chemicals released in the bloodstream to fight the infection trigger inflammatory responses throughout the body. This inflammation can trigger a cascade of changes that damage multiple organ systems, causing them to fail. While the coding for sepsis can be particularly challenging, fortunately, we have the ICD-10-CM Official Guidelines for Coding and Reporting to use as a guide.
Chapter 1 of the ICD-10-CM guidelines provides incredibly detailed instruction on coding for sepsis, severe sepsis, and septic shock infections. The guidelines instruct to first assign the appropriate code for the underlying systemic infection. If the type of infection is not specified, then report code A41.9, Sepsis, unspecified organism. R65.20 (severe sepsis without septic shock) or R65.21 (severe sepsis with septic shock) should only be assigned if severe sepsis is specified when an associated acute organ dysfunction is documented.
Example: Sepsis Coding
An 85-year-old male is admitted with sepsis.
- A41.9 – Sepsis, unspecified organism
Note, only code A41.9, Sepsis, unspecified organism since only sepsis is documented and the type of infection is not specified; but what would you code if the provider documents “85-year-old male is admitted with urosepsis?”
You would not be able to assign a diagnosis code. Instead, you need to query the provider for clarification. The guidelines state, “The term urosepsis is a nonspecific term. It is not to be considered synonymous with sepsis. It has no default code in the Alphabetic Index. Should a provider use this term, he/she must be queried for clarification.”
Severe Sepsis
To accurately assign codes for severe sepsis, refer to sections 1.C.1.d.1.b and 1.C.1.d.3 of the ICD-10-CM Chapter 1 Guidelines which states a minimum of two codes is needed to accurately code for severe sepsis. The first code is for the underlying systemic infection. Once again, if the underlying infection is not specified, report A41.9, Sepsis, unspecified. Next, report a code from subcategory R65.20, severe sepsis without septic shock or R65.21 severe sepsis with septic shock. Then, report the additional code(s) for the associated acute organ dysfunction. Remember, when reporting R65.20 or R65.21 an associated organ dysfunction must be documented.
Example: Severe Sepsis Coding
A 41-year-old female is admitted with sepsis that has caused hypoxic, acute respiratory failure.
- A41.9 – Sepsis, unspecified organism
- R65.20 – Severe sepsis without septic shock
- J96.01 – Acute respiratory failure with hypoxia
First, code the underlying systemic infection (A41.9, Sepsis, unspecified organism). Second, code the severe sepsis as the patient has an acute organ failure associated with the sepsis (R65.20 – severe sepsis without septic shock). Third, code the acute organ dysfunction (J96.01- hypoxic, acute respiratory failure).
Septic Shock
The ICD-10-CM Chapter 1 Guidelines state that septic shock refers to circulatory failure associated with severe sepsis. The guidelines instruct to first code the systemic infection, followed by R65.21, severe sepsis with septic shock. However, if the septic shock is postprocedural, code T81.12, postprocedural septic shock. Note the instructions in the Tabular state septic shock cannot be assigned as a principal diagnosis.
Sepsis or Severe Sepsis with a Localized Infection
If the reason for admission is sepsis or severe sepsis with a localized infection, such as pneumonia, the Guidelines instruct to code the underlying infection as the first diagnosis if the type of infection is not specified assign code A41.9, Sepsis, unspecified. The code for the localized infection should be coded second. If the patient has severe sepsis with a localized infection, report a code from subcategory R65.20 as a secondary diagnosis. However, if the patient is admitted with a localized infection but does not develop sepsis until after the admission, code the localized infection followed by the sepsis/severe sepsis codes.
Example 1: Severe sepsis with localized infection coding
A 41-year-old female is admitted with sepsis with pneumonia that has caused hypoxic, acute respiratory failure.
- A41.9 – Sepsis, unspecified organism
- R65.20 – Severe sepsis without septic shock
- J96.01 – Acute respiratory failure with hypoxia
- J18.9 – Pneumonia, unspecified organism
Assign the underlying systemic infection as the primary diagnosis (A41.9, Sepsis, unspecified organism). Since the patient has an acute organ failure associated with the sepsis, assign R65.20, severe sepsis without septic shock as the second diagnosis. Note, the presence of shock was not documented. Code the acute organ dysfunction (J96.01 – hypoxic, acute respiratory failure) as the third diagnosis with the localized infection (J18.9 – pneumonia) coded as the fourth diagnosis.
Example 2: Severe sepsis with localized infection coding
A 41-year-old female is admitted with urosepsis caused by an Escherichia coli UTI that has caused hypoxic, acute respiratory failure. Diagnosis codes for this example:
- A41.51 – Sepsis due to Escherichia coli [E. coli]
- R65.20 – Severe sepsis without septic shock
- J96.01 – Acute respiratory failure with hypoxia
- N39.0 – Urinary tract infection, site not specified
First, assign code A41.51, sepsis due to Escherichia coli [E. coli] for the underlying systemic infection. Since the patient has an acute organ failure associated with the sepsis, assign R65.20, severe sepsis without septic shock as the second diagnosis. Note, the presence of shock was not documented. Then, assign J96.01, hypoxic, acute respiratory failure for the organ failure as the third diagnosis and code N39.0, urinary tract infection, site not specified for the local infection as the fourth diagnosis.
You may be wondering why we would not code B96.20, Unspecified Escherichia coli [E. coli] since there is a “use additional code” note under code N39.0 in the Tabular. See the question and answer below from Coding Clinic for ICD-10-CM/PCS, First Quarter 2018, page 16:
Question:
A patient with mental status change is admitted and after diagnostic studies, the provider diagnosed sepsis due to Escherichia coli (E. coli) urinary tract infection (UTI). What are the appropriate code assignments for this diagnostic statement? There is confusion among coding professionals regarding the application of the instructional note stating: “Use additional code (B95-B97), to identify infectious agent” at code N39.0, Urinary tract infection, site not specified, versus assigning a code that identifies both sepsis and the infectious agent.
Answer:
Assign code A41.51, Sepsis due to Escherichia coli [E. coli], and code N39.0, Urinary tract infection, site not specified, for the UTI.
Do not assign code B96.20, Unspecified Escherichia coli [E. coli] as the cause of diseases classified elsewhere, as an additional diagnosis. Code A41.51 clearly identifies the causal bacterium for both the sepsis and the UTI. Assigning B96.20 as an additional code is redundant.”
Sepsis Due to a Postprocedural Infection
Several questions must be answered before coding sepsis due to a post-procedural infection.
- Was the procedure obstetrical?
- Is the site of the infection documented?
- Is the infectious agent documented?
- Is severe sepsis or acute organ dysfunction documented?
If it is known that the procedure was non-obstetrical and the site of the infection is documented, assign a code from T81.40-T81.43 as our primary code. Then, code T81.44, Sepsis following a procedure, as the second code. For the third diagnosis, code the underlying infection, or A41.9, if the type of infection is not documented. If the documentation stated severe sepsis or if there was a sepsis-associated acute organ dysfunction, code R65.20, along with the code for the organ dysfunction.
If the procedure was obstetrical and the site of the infection is documented, assign a code from O86.00-O86.03 as the primary code. Then, code O86.04, Sepsis following an obstetric procedure as the second code. For the third diagnosis, code the underlying infection or A41.9 if the type of infection is not documented. If the documentation stated severe sepsis or if there was a sepsis associated acute organ dysfunction, code R65.20 along with the code for the organ dysfunction.
For infections following infusion, transfusion, therapeutic injection, or immunization, assign a code from subcategory T80.2, Infections following infusion, transfusion, and therapeutic injection, or code T88.0-, Infection following immunization. Then assign a code for the specific infection. If severe sepsis is documented, assign the appropriate code from subcategory R65.2 along with the additional codes(s) for any acute organ dysfunction.
Example: Sepsis due to a postprocedural infection coding
A 52-year-old male is admitted with sepsis due to a post-operative infection of the small intestine, following an appendectomy.
- T81.43XA – Infection following a procedure, organ, and space surgical site, initial encounter
- T81.44XA – Sepsis following a procedure, initial encounter
- A41.9 – Sepsis, unspecified organism
Assign T81.43XA, infection following a procedure, organ and space surgical site, initial encounter as the first diagnosis, this is the site of the infection. Then, assign code T81.44XA, Sepsis following a procedure, initial encounter as our second diagnosis. Finally, code A41.9, Sepsis unspecified organism as the third diagnosis.
Postprocedural Infection and Postprocedural Septic Shock
If a post-procedural infection results in septic shock, the ICD-10-CM Chapter 1 Guidelines instructs to first code the sepsis due to postprocedural infection (see codes above), followed by code T81.12-, Postprocedural septic shock. The guidelines state not to assign code R65.21, Severe sepsis with septic shock. Additional code(s) should be assigned for any acute organ dysfunction.
Example: Postprocedural infection and postprocedural septic shock coding
A 52-year-old male is admitted with septic shock due to a post-operative infection of the small intestine following an appendectomy that has caused acute liver failure.
- T81.43XA – Infection following a procedure, organ, and space surgical site, initial encounter
- T81.44XA – Sepsis following a procedure, initial encounter
- A41.9 – Sepsis, unspecified organism
- T81.12XA – Postprocedural septic shock, initial encounter
- K72.00 – Acute and subacute hepatic failure without coma
Frist, assign the site of the infection as the first diagnosis T81.43XA – Infection following a procedure, organ and space surgical site, initial encounter. Next, assign T41.44XA for sepsis following a procedure (Sepsis following a procedure, initial encounter). Code A41.9, Sepsis, unspecified organism as the third diagnosis, per the instructions under diagnosis T81.44- that state to use an additional code to identify the sepsis. The fourth diagnosis code is T81.12XA, Postprocedural septic shock, initial encounter. The fifth and final code is K72.00, Acute and subacute hepatic failure without coma, for the acute organ dysfunction.
Sepsis and Severe Sepsis Associated with a Noninfectious Process (condition)
Per ICD-10-CM Chapter 1 Guideline I.C.1.d.6., “In some cases, a noninfectious process (condition) such as trauma, may lead to an infection which can result in sepsis or severe sepsis. If sepsis or severe sepsis is documented as associated with a noninfectious condition, such as a burn or serious injury, and this condition meets the definition for principal diagnosis, the code for the noninfectious condition should be sequenced first, followed by the code for the resulting infection. If severe sepsis is present, a code from subcategory R65.2 should also be assigned with any associated organ dysfunction(s) codes. It is not necessary to assign a code from subcategory R65.1, Systemic inflammatory response syndrome (SIRS) of non-infectious origin, for these cases.
If the infection meets the definition of principal diagnosis, it should be sequenced before the non-infectious condition. When both the associated non-infectious condition and the infection meet the definition of principal diagnosis, either may be assigned as principal diagnosis.
Only one code from category R65, Symptoms and signs specifically associated with systemic inflammation and infection, should be assigned. Therefore, when a non-infectious condition leads to an infection resulting in severe sepsis, assign the appropriate code from subcategory R65.2, Severe sepsis. Do not additionally assign a code from subcategory R65.1, Systemic inflammatory response syndrome (SIRS) of non-infectious origin.”
Example: Sepsis and severe sepsis associated with a noninfectious process (condition) coding
A 68-year-old female is admitted with a traumatic subdural hematoma and developed sepsis with acute kidney failure 3 days after the admission.
- S06.5XAA – Traumatic subdural hemorrhage with loss of consciousness status unknown, initial encounter
- A41.9 – Sepsis, unspecified organism
- R65.20 – Severe sepsis without septic shock
- N17.9 – Acute kidney failure, unspecified
We would assign S06.5XAA, Traumatic subdural hemorrhage with loss of consciousness status unknown, initial encounter as the primary diagnosis, because the patient was admitted for a noninfectious condition. We would code A41.9 as the second diagnosis because the sepsis did not occur until three days after the admission. We would code the R65.20 as the third diagnosis because there was an acute organ dysfunction associated with the sepsis Finally, we would code N17.9, Acute kidney failure, unspecified as the fourth diagnosis.
Additional Sepsis Guidelines from Chapter 15
Not all sepsis related guidelines are found in chapter 1. Chapter 15 also discusses sepsis coding.
Sepsis and Septic Shock Complicating Abortion, Pregnancy, Childbirth, and the Puerperium
The sepsis coding guideline in Chapter 15(I.C.15.j) is like those in chapter 1. We would assign the code for sepsis complicating abortion, pregnancy, childbirth, and the puerperium as our primary code. Then we would code the specific type of infection or A41.9 if the type is not documented as our second diagnosis. After that we would code R65.2, Severe sepsis if severe sepsis (or an acute organ dysfunction associated with sepsis) is documented. Then we would code the associated acute organ dysfunction.
Example: Sepsis and septic shock complicating abortion, pregnancy, childbirth, and the puerperium coding
A 24-year-old female presents with sepsis due to an intraabdominal abscess that developed 3 days after a scheduled C-section. Diagnosis codes for this example:
- O86.03 – Infection of obstetric surgical wound, organ, and space site
- O86.04 – Sepsis following an obstetrical procedure
- A41.9 – Sepsis, unspecified organism
Assign the site of the infection as the first diagnosis (Infection of obstetric surgical wound, organ, and space site – O86.03). Then, assign the additional code for sepsis following a procedure (Sepsis following an obstetrical procedure – O86.04). Per the instructions under diagnosis O86.04, use an additional code to identify the sepsis (Sepsis, unspecified organism – A41.9).
Puerperal Sepsis
Per ICD-10-CM Chapter 15 guideline I.C.15.k. Code O85, Puerperal sepsis, should be assigned with a secondary code to identify the causal organism (e.g., for a bacterial infection, assign a code from category B95-B96, Bacterial infections in conditions classified elsewhere). A code from category A40, Streptococcal sepsis, or A41, Other sepsis, should not be used for puerperal sepsis. If applicable, use additional codes to identify severe sepsis (R65.2-) and any associated acute organ dysfunction.
Code O85 should not be assigned for sepsis following an obstetrical procedure (See Section I.C.1.d.5.b., Sepsis due to a postprocedural infection).
Example: Puerperal sepsis coding
A 31-year-old female was admitted with postpartum sepsis (7 days postpartum) with associated respiratory failure.
- O85 – Puerperal sepsis
- R65.20 – Severe sepsis without septic shock
- J96.00 – Acute respiratory failure, unspecified whether with hypoxia or hypercapnia
Following the Chapter 15 ICD-10-CM Guideline above for puerperal sepsis, assign O85Puerperal sepsis as the first diagnosis. Note, there was no causal organism identified but since the patient has acute organ dysfunction, assign R65.20, Severe sepsis as the second diagnosis. Code J96.00, Acute respiratory failure, unspecified whether hypoxia or hypercapnia as the third diagnosis to identify the acute organ dysfunction.
The key to successfully coding sepsis lies in keeping a copy of the ICD-10-CM Guidelines on hand. You can find these guidelines in the front of your ICD-10-CM codebook. To download a PDF version of the 2023 Guidelines, click here.
Additional AHA Coding Clinic Clarification
Viral Sepsis (Coding Clinic, Third Quarter 2016: Page 8)
Question:
How would viral sepsis be coded in ICD-10-CM? The type of viral infection is unspecified. In ICD-9-CM, “Viral” was a sub term under septicemia, but it is not present as a sub term under sepsis in ICD-10-CM. By selecting “sepsis with specified organism NEC” code A41.89 is referenced. However, in ICD-10-CM, categories A30-A49 encompass “other bacterial diseases.” Would it be appropriate to assign a bacterial code for a viral condition?
Answer:
Assign codes A41.89, Other specified sepsis, and B97.89, Other viral agents as the cause of diseases classified elsewhere. Although codes in categories A30-A49 classify bacterial illnesses, there is no specific code for viral sepsis. “Sepsis, specified organism NEC” is indexed to code A41.89. Code A41.89 is the best available option to capture the concept of sepsis, since ICD-10-CM does not have a specific code for viral sepsis, along with code B97.89 to provide an additional level of specificity when the virus is not specified.
Sepsis due to Aspiration Pneumonia (Coding Clinic for ICD-10-CM/PCS, Second Quarter 2020: Page 28)
Question:
When the provider documents “sepsis due to aspiration pneumonia,” is a code for the sepsis, or the aspiration pneumonia assigned as the principal diagnosis?
Answer:
Assign code A41.9, Sepsis, unspecified organism, as the principal diagnosis. Codes J18.9, Pneumonia, unspecified organism, and J69.0, Pneumonitis due to inhalation of food and vomit, should be assigned as additional diagnoses. Sepsis indicates infection and the body’s response to it. Aspiration pneumonia may be just from the direct effect of inhaled material, such as a chemical effect, or it may involve infection; however, for sepsis to result, it would need to involve an infectious pneumonia. Therefore, codes J18.9 and J69.0 are both needed to show the presence of a localized infection (pneumonia and unspecified organism) as well as pneumonia due to aspiration. When sepsis and aspiration pneumonia are related (i.e., sepsis due to aspiration pneumonia or sepsis related to aspiration pneumonia) and present on admission, sepsis should be sequenced as the principal diagnosis.
Tips and Reminders:
- Always read the full ICD-10-CM chapter-specific coding guidelines for sepsis in chapters 1 and 15 (if applicable).
- Always read any coding instructions under the diagnosis codes for “code-first” and “use additional” code notes.
- Review any pertinent AHA Coding Clinic(s) that pertain to sepsis.
References:
ICD-10-CM Chapters 1 and 15 2023 ICD-10-CM Documentation Guidelines
Coding Clinic for ICD-10-CM/PCS, First Quarter 2018: Page 16
Coding Clinic, Third Quarter 2016: Page 8