Sepsis, Severe Sepsis, and Septic Shock: How Many Codes, and Which Goes First

Section I.C.1.d of the Official Guidelines treats sepsis, severe sepsis and septic shock as three different coding problems, and the number of codes changes at each step.

Sepsis: one code

“For a diagnosis of sepsis, assign the appropriate code for the underlying systemic infection. If the type of infection or causal organism is not further specified, assign code A41.9, Sepsis, unspecified organism.”

There is no separate “sepsis” code added on top of the infection — the infection code is the sepsis code. A41.9 is the default only when nothing more specific is documented; a streptococcal sepsis belongs in A40.-, and category A41 carries an Excludes1 sending it there.

Severe sepsis: at least two codes

“The coding of severe sepsis requires a minimum of 2 codes: 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 are also required.”

The tabular writes the same instruction into R65.2 itself: a Code First note for the underlying infection, and a Use Additional Code note listing the organ-dysfunction codes — acute kidney failure (N17.-), acute respiratory failure (J96.0-), critical illness myopathy and polyneuropathy, DIC (D65), septic encephalopathy (G93.41), hepatic failure (K72.0-). The threshold for using R65.2- at all is documentation: “A code from subcategory R65.2, Severe sepsis, should not be assigned unless severe sepsis or an associated acute organ dysfunction is documented.”

Septic shock: severe sepsis plus R65.21

“Septic shock generally refers to circulatory failure associated with severe sepsis, and therefore, it represents a type of acute organ dysfunction. For cases of septic shock, the code for the systemic infection should be sequenced first, followed by code R65.21, Severe sepsis with septic shock or code T81.12, Postprocedural septic shock. Any additional codes for the other acute organ dysfunctions should also be assigned. As noted in the sequencing instructions in the Tabular List, the code for septic shock cannot be assigned as a principal diagnosis.”

The sequencing rule is the same for every tier, and it is absolute for R65.2-:

“If severe sepsis is present on admission, and meets the definition of principal diagnosis, the underlying systemic infection should be assigned as principal diagnosis followed by the appropriate code from subcategory R65.2 as required by the sequencing rules in the Tabular List. A code from subcategory R65.2 can never be assigned as a principal diagnosis. When severe sepsis develops during an encounter (it was not present on admission), the underlying systemic infection and the appropriate code from subcategory R65.2 should be assigned as secondary diagnoses.”

So present-on-admission status decides whether the infection is principal or secondary, but never whether R65.2- leads — it cannot. When the record does not say whether severe sepsis was present on admission, the Guidelines say to query, noting that “the diagnosis may not be confirmed until sometime after admission.”

Sepsis with a localized infection

“If the reason for admission is sepsis or severe sepsis and a localized infection, such as pneumonia or cellulitis, a code(s) for the underlying systemic infection should be assigned first and the code for the localized infection should be assigned as a secondary diagnosis. … If the patient is admitted with a localized infection, such as pneumonia, and sepsis/severe sepsis doesn’t develop until after admission, the localized infection should be assigned first, followed by the appropriate sepsis/severe sepsis codes.”

Timing, again, is what moves the order: sepsis on admission puts the systemic infection first; pneumonia on admission with sepsis developing later puts the pneumonia first.

Discharge documentation: sepsis, organism not identified, with acute kidney failure attributed to the sepsis, both present on admission. No shock.

1. A41.9 — Sepsis, unspecified organism (principal)
2. R65.20 — Severe sepsis without septic shock (secondary; R65.2’s Code First note points back to A41.9)
3. N17.9 — Acute kidney failure, unspecified (secondary; the organ dysfunction R65.2’s Use Additional note asks for)

Change one fact and the codes change. If the kidney failure is documented as due to something other than the sepsis, R65.20 is not assigned at all — “An acute organ dysfunction must be associated with the sepsis in order to assign the severe sepsis code,” and if the relationship is unclear, query. If shock is documented, R65.21 replaces R65.20. If the sepsis developed after admission for something else, A41.9 and R65.20 both become secondary and the admitting condition is principal.

Postprocedural sepsis reverses the usual order: the complication code leads, and the sepsis is added to it.

“For sepsis following a postprocedural wound (surgical site) infection, a code from T81.41 to T81.43, Infection following a procedure, T81.49, Infection following a procedure, other surgical site, or a code from O86.00 to O86.03 … that identifies the site of the infection should be sequenced first, if known. Assign an additional code for sepsis following a procedure (T81.44) or sepsis following an obstetrical procedure (O86.04). Use an additional code to identify the infectious agent. If the patient has severe sepsis, the appropriate code from subcategory R65.2 should also be assigned with the additional code(s) for any acute organ dysfunction.”

T81.44 carries its own Use Additional Code note “to identify the sepsis,” and categories A40 and A41 carry the reciprocal Code First for postprocedural sepsis (T81.44-). Code assignment here rests on the provider documenting the relationship between the infection and the procedure.

Shock after a procedure has its own code, and the Guidelines forbid the general one:

“If a postprocedural infection has resulted in postprocedural septic shock, assign the codes indicated above for sepsis due to a postprocedural infection, followed by code T81.12-, Postprocedural septic shock. Do not assign code R65.21, Severe sepsis with septic shock.”

The tabular enforces the same thing from the other side — R65.21 carries an Excludes1 for postprocedural septic shock (T81.12-). The pair R65.21 with T81.12 is one Claim Check users bring, and the answer is never “both”: shock following a procedure is T81.12-, and R65.21 comes off.

• “Urosepsis.” “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.” There is no code to assign from the word alone.
• Negative blood cultures. “Negative or inconclusive blood cultures do not preclude a diagnosis of sepsis in patients with clinical evidence of the condition; however, the provider should be queried.”
• Bacteremia is not sepsis.R78.81, Bacteremia, carries an Excludes1 reading “sepsis-code to specified infection,” and A41 excludes bacteremia NOS in return. The two are mutually exclusive by note; the documentation decides which one the patient has.
• Only one R65 code. When a noninfectious condition such as trauma or a burn leads to an infection and then to 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.” R65.1 carries the matching Excludes1 for sepsis and severe sepsis. Which condition is principal — the noninfectious one or the infection — follows the ordinary principal-diagnosis test, and “when both … meet the definition of principal diagnosis, either may be assigned.”
• Hemolytic-uremic syndrome. When the reason for admission is HUS associated with sepsis, D59.31 is principal and the infection and severe-sepsis codes are secondary.
• Newborn and obstetric sepsis have their own chapters: P36.- (bacterial sepsis of newborn, with its own Use Additional note for R65.2-) and O85 (puerperal sepsis). A41 excludes both.

The classification rule — R65.2- is never principal — has a payer echo. The Medicare Code Editor’s edit 09 (unacceptable principal diagnosis) lists R65.20, R65.21, R65.10, R65.11 and T81.12XA; it does not list A41.9 or T81.44XA. A Medicare inpatient claim that leads with a severe-sepsis or septic-shock code fails the edit, and it would also have been sequenced wrongly under the Guidelines. The edit is a consequence of the rule, not a second rule: sequence per Section I.C.1.d and the edit takes care of itself.

1. Confirm the diagnosis: sepsis, severe sepsis, or septic shock — and remember “urosepsis” is not a diagnosis (query).
2. Code the systemic infection; A41.9 if the organism is not documented.
3. If severe sepsis or an associated acute organ dysfunction is documented, add R65.20 (R65.21 with shock) after the infection, then a code for each organ dysfunction.
4. Sequence by present-on-admission status: infection principal when severe sepsis was present on admission and meets the definition; both secondary when it developed later. R65.2- is never principal.
5. For a localized infection on admission with later sepsis, the localized infection leads; for postprocedural sepsis, the T81.4- site code leads and T81.12- replaces R65.21 for shock.
6. Query when organ-dysfunction attribution, POA status, or the diagnosis itself is unclear.

• R65.2- as principal diagnosis.
• A code for “urosepsis.”
• Omitting the organ-dysfunction codes required with R65.2-.
• R65.21 for shock after a procedure — T81.12- instead.
• Assigning R65.2- when the organ dysfunction is documented as due to another condition.
• Assigning both R65.1- and R65.2- — only one R65 code.

• The word “sepsis” (or a specific systemic infection), and the organism if known.
• Severe sepsis, or an acute organ dysfunction linked to the sepsis.
• Septic shock.
• Present-on-admission status of the sepsis / severe sepsis.
• A procedural cause and the surgical-site infection.
• A localized infection and which came first.