Coding for Sepsis in ICD-10

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Coding a diagnosis of sepsis can be a tricky proposition. There are several guidelines to consider and documentation must be reviewed carefully. Below is an overview of some of the guidelines with examples of guideline application.

The guidelines for coding sepsis, severe sepsis and septic shock are found in the chapter specific coding guidelines for chapter 1 of ICD-10; Certain Infectious and Parasitic Diseases. Coverage of this topic encompasses guidelines I.C.1.d.1.a – I.C.1.d.8. This post focuses on 4 of those guidelines.

I.C.1.d.1.a – Sepsis

Coding sepsis that is not further specified as severe sepsis, sepsis with acute organ dysfunction or sepsis with septic shock requires the assignment of a single code for the underlying systemic infection. If the underlying infection or causative organism is not further specified, assign code A41.9; Sepsis unspecified organism.

Diagnosis: E coli sepsis = A41.51

A41.51; Sepsis due to Eschericia Coli is assigned because this is the code the index references for the systemic infection of E.Coli sepsis.

I.C.1.d.1.b – Severe Sepsis

Coding sepsis that is further specified as severe sepsis or sepsis with acute organ dysfunction requires the assignment of a minimum of two codes, a code for the underlying systemic infection and code from subcategory R65.2; Severe sepsis. Additional codes for any associated acute organ dysfunction should also be assigned.

Note that the codes from subcategory R65.2 can never be assigned alone and can never be sequenced as principal. They will always be assigned in conjunction with and sequenced after the code for the systemic infection.

Diagnosis: Sepsis with acute renal and respiratory failure = A41.9, R65.20, N17.9, J96.00

The correct sepsis code for this example is A41.9 because the organism causing the underlying systemic infection is not specified.

Although the sepsis is not specified as severe a code from subcategory R65.2; Severe Sepsis is appropriate as indicated by guideline I.C.1.d.1.a.iii which directs the coder to follow the guidelines for the coding of severe sepsis when coding a diagnosis of sepsis with acute organ dysfunction. The correct 5th character for this code is “0” because septic shock was not documented.

Additional codes are assigned for the acute renal and respiratory failure.

I.C.1.d.2 – Septic Shock

Septic shock in and of itself is a type of acute organ dysfunction and should therefore be coded according to the guidelines for the coding of severe sepsis. In this case the 5th character for the code from subcategory R65.2 will be a “1”, indicating severe sepsis with septic shock. If other acute organ dysfunction is present, additional codes should be assigned for those conditions.

Diagnosis: Pseudomonal septic shock = A41.52, R65.21

Coding this diagnosis requires only two codes as R65.21 is a combination code that reports both severe sepsis and septic shock.

I.C.1.d.4 - Sepsis and severe sepsis with a localized infection

Sepsis often stems from a localized infection. When both a localized infection (e.g., pneumonia or UTI) and associated sepsis/severe sepsis are present on admission, the code for the systemic infection is sequenced first and the code for the localized infection is sequenced as a secondary code. If the sepsis is severe and additional code R65.2 code and any applicable codes for acute organ dysfunction should be assigned.

Diagnosis: Patient admitted with sepsis secondary to staphylococcal pneumonia = A41.2, J15.20

If the patient is admitted with a localized infection and sepsis/severe sepsis develops after admission, code the localized infection first followed by the appropriate sepsis coding as secondary codes.

Diagnosis: Patient admitted for acute pyelonephritis secondary to Enterococcus. During admission, the pyelonephritis advanced to severe sepsis with acute renal failure = N10, B95.2, A41.81, R65.20, N17.9

Coding this scenario requires 5 codes. The acute enterococcal pyelonephritis is coded first because it was the reason for admission. This diagnosis needs two codes, a code for the acute pyelonephritis and a code that identifies the causative organism. Because the severe sepsis developed after admission the sepsis codes are sequenced following the codes for the localized infection. This diagnosis requires 3 codes, a code for the systemic infection, a code for severe sepsis without septic shock and a code for the acute organ dysfunction.

While coding for sepsis can be complicated; knowing, understanding, and following the coding guidelines for sepsis, will lead the coder to accurate coding outcomes.

Leave a comment below »

  1. nicky January 05, 2017

    when coding severe sepsis, I always see examples of acute renal failure or respiratory failure as the acute organ dysfunction…but that isn’t an all inclusive list correct? if the surviving sepsis guidelines indicate that Lactic Acid >4 is an indicator of septic shock…then what is the code used for the acute organ dysfunction to go along with severe sepsis?

  2. CodingSupport January 09, 2017

    Hi Nicky,

    The coding of severe sepsis requires a minimum of 2 odes: first a code for the underlying systemic infection, followed by a code from subcategory R65.2, severe sepsis.  If the causal organism is not documented, assign code A41.9, Sepsis, unspecified organism, for the
    infection.  Additional code(s) for the associated acute organ dysfunction a
    re also required.
    Due to the complex nature of severe sepsis, some cases
    may require querying the provider prior to assignment of
    the codes.
    Coding Guidelines Chapter 1.d.a.b

    Hope this helps!

  3. Mark January 26, 2017

    How would you code sepsis associated with recent amputation infection?

  4. Instructor January 26, 2017


    We are going to use a T81.4 code for infection following a procedure. Followed by the code for the specific infection if known. If the organism is not know, you will use A41.9.

    Good luck with your studies!



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