Conquer Coding for Sepsis and SIRS

Arm yourself with a solid understanding of key terms and guidelines to overcome sepsis coding hurdles.

Sepsis, systemic inflammatory response syndrome (SIRS), and septicemia have historically been difficult to code. Changing terminology, evolving definitions, and guideline updates over the past 20 years have created confusion with coding sepsis. Much has changed since I wrote my first sepsis article in 2015, and it’s imperative to keep up with the changes to sepsis and SIRS ICD-10-CM coding.

In 2016, Sepsis-3 criteria were revealed as a result of The Third International Consensus Definitions for Sepsis and Septic Shock. We saw the addition of Chapter 22 in ICD-10-CM (U codes) in 2020, and now COVID-19 has further muddied the turbid waters of sepsis coding.

Despite these changes, one thing has remained the same — sepsis is still a beast to code, and documentation for it is often inadequate. Yet, it is now more than ever critical to code sepsis properly due to the impact a sepsis diagnosis has on reimbursement, especially given the recent financial difficulties healthcare facilities are facing due to the COVID-19 pandemic. This article will shed light on coding for sepsis and related conditions using actual inpatient case studies and example scenarios from an acute care hospital.

Diagnoses Affect Reimbursement

The best way to see how a sepsis diagnosis can impact reimbursement is by example. Consider this case study:

A 79-year-old patient presented to the emergency department (ED) with shortness of breath and was admitted with a diagnosis of community-acquired pneumonia. The vital signs and lab work done in the ED revealed that the patient had a fever, tachypnea, and leukocytosis, and the chest X-ray showed infiltrates. The sputum culture was positive for Pseudomonas aeruginosa. The patient had a six-day length of stay. The discharge diagnoses were Pseudomonas pneumonia, lactic acidosis, asthma exacerbation, hypoxemia, and chronic bronchitis. “Possible sepsis” was documented in the consulting physician’s note only.

As the documentation stands, the ICD-10 codes are:

J15.1     Pneumonia due to Pseudomonas

J45.901 Unspecified asthma with (acute exacerbation) (Note: J45.901 is designated as a complication and comorbidity by CMS.)

E87.2     Acidosis (Note: E87.2 is designated as a complication and comorbidity by CMS.)

R09.02  Hypoxemia

J42        Unspecified chronic bronchitis

Medicare Severity Diagnosis Related Group (MS-DRG): 178, $12,916.47

Now, let’s see what would happen if the coder queried the physician about a sepsis diagnosis and the provider confirmed that the patient had sepsis. The chart would then be coded as:

A41.9    Sepsis, unspecified organism






MS-DRG: 871, $19,682.62

The difference in reimbursement between the two scenarios for this hospital encounter is $6,766.15.

Sepsis Defined

Sepsis is a potentially life-threatening condition that occurs when the body’s response to an infection damages its own tissues. Without timely treatment, sepsis can progress rapidly and lead to tissue damage, organ failure, and then death. Proper coding of sepsis and SIRS requires the coder to understand the stages of sepsis and common documentation issues.

Localized Infection

Almost any type of infection can lead to sepsis. Infections that lead to sepsis most often start in the lung, urinary tract, skin, or gastrointestinal tract. When localized infections are contained, they tend to be self-limiting and resolve with antibiotics. It’s important to identify and treat localized infections promptly, otherwise, sepsis may develop. Occasionally, the source of sepsis cannot be determined during the inpatient stay, but sepsis should be coded when it is adequately documented.

Documentation issues: A patient with a localized infection usually presents with tachycardia, leukocytosis, tachypnea, and/or fever. These are typical symptoms of any infection. It is up to the clinical judgment of the physician to decide whether the patient has sepsis. The coder cannot assume the patient has sepsis based on the criteria being met; they must rely on the physician’s documentation (ICD-10-CM guideline I.A.19). A query can be initiated when the patient meets SIRS criteria and has a localized infection but no documentation of sepsis.

Coding tips: Per ICD-10-CM guideline I.C.1.d.4, if a patient is admitted with localized infection and sepsis or severe sepsis, assign the code for the systemic infection (i.e., sepsis) first, followed by a code for the localized infection when sepsis meets the definition of a principal diagnosis. 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, if applicable.

According to AHA Coding Clinic® (Vol. 1, No. 3, p. 4), when a patient has SIRS and a localized infection, sepsis can no longer be coded and an ICD-10-CM code for sepsis cannot be assigned unless the physician specifically documents sepsis. In the ICD-10-CM Alphabetic Index, under Syndrome/systemic inflammatory response, the only options are for “of non-infectious origin” without (R65.10 Systemic inflammatory response syndrome of non-infectious origin without acute organ dysfunction) or with acute organ dysfunction codes (R65.11 Systemic inflammatory response syndrome (SIRS) of non-infectious origin with acute organ dysfunction).

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

J18.9     Pneumonia, unspecified organism

J96.01   Acute respiratory failure with hypoxia


N17.9    Acute kidney failure, unspecified

R65.21  Severe sepsis with septic shock


Bacteremia is a microbiological lab finding of bacteria in the blood. When a patient is diagnosed solely with bacteremia, it means that they are not showing any clinical signs of sepsis or SIRS. Bacteremia may be transient, or it can lead to sepsis. When a patient’s blood cultures are positive, but the physician does not believe it to be a contaminant, the patient is treated with antibiotics.

Documentation issues: The ICD-10-CM code for bacteremia is R78.81 Bacteremia. If the patient has bacteremia with sepsis, the Alphabetic Index directs the coder to “see Sepsis.” When both bacteremia and sepsis are documented, code sepsis only.

Coding tips: According to ICD-10-CM guideline I.B.4, if bacteremia is associated with a local infection, code first the local infection, followed by the code for bacteremia, and then the infectious organism. Note that R78.81 is a sign-and-symptom code from Chapter 18 so it cannot be coded as the principal diagnosis when a definitive diagnosis has been documented.

Example: A 79-year-old patient is admitted with dizziness and dysuria. A urine sample is collected on admission and is positive for Klebsiella pneumoniae. The blood sample, taken on admission, is also positive for Klebsiella. The doctor lists: Urinary tract infection (UTI) due to Klebsiella, bacteremia due to Klebsiella. Correct coding is:


N39.0    Urinary tract infection, site not specified

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


Septicemia, also known as blood poisoning, is a serious infection of the blood. Usually, it is caused by the presence of bacteria or toxins in the blood, but it can also be caused by fungal, parasitic, or viral infections. In contrast to bacteremia, where the patient is asymptomatic, septicemia causes symptoms and is a clinical diagnosis. Septicemia is not just a transient lab finding; the patient has symptoms, and the condition warrants inpatient admission with antibiotics and supportive treatment.

Documentation issues: Septicemia is rarely a term physicians document. To reflect this shift in terminology, when you look up the term septicemia in the ICD-10-CM Alphabetic Index, you are told to “see Sepsis.” Under the entry for sepsis in ICD-10-CM are the various causative organisms and septic conditions.

Example: A 39-year-old woman is admitted with high fever, leukocytosis, malaise, and myalgias. Blood and urine cultures taken on admission are positive for Escherichia coli (E. coli). The patient is diagnosed with septicemia and urinary tract infection due to E. coli. Correct coding is:

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


Systemic Inflammatory Response Syndrome

SIRS is an inflammatory state affecting the whole body. It is an exaggerated defense response of the body to a noxious stressor, such as infection or trauma, that triggers an acute inflammatory reaction, which may progress and result in the formation of blood clots, impaired fibrinolysis, and organ failure. Patients with SIRS will have two or more of the following symptoms: tachycardia, tachypnea, leukocytosis or leukopenia, and fever or (rarely) hypothermia.

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
  • White blood cells > 12,000 cell/mm3 or < 4,000 cells/mm3

Documentation issues: When SIRS is documented with an inflammatory condition, such as pancreatitis, the inflammatory condition should be sequenced first, followed by the code for SIRS, R65.1-. When SIRS is documented with an infectious source, for instance, “SIRS due to pneumonia,” only code pneumonia. However, a query for sepsis may be appropriate according to AHA Coding Clinic® (Vol. 1, No. 3, p. 4).

Coding tips: SIRS can be due to noninfectious causes or infectious causes. When SIRS is due to a noninfectious process, code first the noninfectious process, followed by the code for SIRS. If organ dysfunction is documented, code also R65.11 and the code(s) for the specific organ dysfunction. When it is unclear whether the acute organ dysfunction is related to SIRS, query the provider (guideline I.C.18.g).

Code R65.10 or R65.11 as the principal diagnosis only in the rare instance when the physician documents that they are unable to determine the underlying cause of SIRS.

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

K85.90  Acute pancreatitis without necrosis or infection, unspecified



Sepsis is an extreme response to infection that develops when the chemicals the immune system releases into the bloodstream to fight infection cause widespread inflammation. This inflammation can lead to blood clots and leaky blood vessels, and without timely treatment, may result in organ dysfunction and then death. Severe cases of sepsis often result from a body-wide infection that spreads through the bloodstream, but sepsis can also be triggered by an infection in the lungs, stomach, kidneys, or bladder. Thus, it is not necessary for blood cultures to be positive to code sepsis (guideline I.C.1.d.1.a.i).

Documentation issues: The coder can assign a code for sepsis when the term “sepsis” is documented by the physician. Clinical indicators for sepsis need not be present to code sepsis. The physician’s documentation that the patient has sepsis is sufficient (guideline I.A.19). 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 in the discharge summary. When sepsis is well documented, and not documented as uncertain in subsequent progress notes or ruled out, you can code sepsis even though it is not documented in the discharge summary. If the documentation for sepsis is unclear or conflicting, query the provider.

Coding tips: Only one code is needed to report sepsis without organ dysfunction. Most sepsis codes are listed in A40.- through A41.9. If a causal organism is specified, then use the code for sepsis naming the specific organism. Per AHA Coding Clinic® (Vol. 5, No. 1, p. 16), when sepsis is linked to an infection with an organism, assign the combination code for sepsis including the organism. For example, sepsis due to E. coli UTI can be coded as A41.51 and N39.0.

Sepsis can be caused by fungi, candida, or viruses, as well. It is 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, you would report B37.7 Candidal sepsis for the principal diagnosis and B37.49 Other urogenital candidiasis for the secondary diagnosis. Do not select a code from A40.- through A41.9.

Example: A 45-year-old woman presents with severe stomachache, fever, vomiting, and bloating. The CT scan reveals a perforated bowel with an abscess. The patient has sepsis and meets SIRS criteria with a peritoneal abscess as the source. The peritoneal fluid and blood cultures are positive for Enterococcus (Group D Strep). Code this as:

A41.81  Sepsis due to Enterococcus

K65.1    Peritoneal abscess

K63.1    Perforation of intestine (non-traumatic)

Viral Sepsis

Sepsis due to a virus is not found as a subterm in the Alphabetic Index. This has raised many questions when coding sepsis due to the influenza and COVID-19 viruses. AHA Coding Clinic® (Vol. 3, No. 3, p. 8) advises using A41.89 Other specified sepsis for sepsis due to viral infections even though this code is found in the Other Bacterial Diseases section (A30-A49) of Chapter 1. When sepsis occurs with COVID-19, follow guidelines I.C.1.d.1-4 for sequencing.

Example: A 59-year-old male presents with generalized muscle aches, coughing, and fever and is diagnosed with sepsis due to acute viral bronchitis due to influenza A. Report these codes:


J10.1     Influenza due to other identified influenza virus with other respiratory manifestations

J20.8     Acute bronchitis due to other specified organisms

Severe Sepsis

Severe sepsis is sepsis with acute organ dysfunction. It occurs when one or more of the body’s organs is damaged from the inflammatory response. Any organ can be affected.

The organ dysfunctions commonly associated with severe sepsis are listed in the ICD-10-CM Tabular List under code category R65.- Symptoms and signs specifically associated with systemic inflammation and infection. This list is not comprehensive. Examples of acute organ dysfunction that are not included on the list are non-ST elevation myocardial infarction (NSTEMI), atrial fibrillation, and thrombocytopenia.

Documentation issues: The physician must document that a condition is acute organ dysfunction related to sepsis for you to code R65.20 Severe sepsis without septic shock. If the physician documents “sepsis with evidence of organ dysfunction” or “sepsis with multi-organ dysfunction,” but does not specifically name the organ dysfunction, you cannot report R65.2- Severe sepsis.

It may be appropriate to query the physician regarding the specific type of organ dysfunction the patient had. Guideline I.C.1.d.a states that R65.2- can be coded when severe sepsis or an associated organ dysfunction is documented. If  “severe sepsis” is documented without mention of organ dysfunction, R65.2- can still be coded, but it is a good practice to query the physician for more information on the organ(s) affected by sepsis.

Occasionally, organ dysfunction, such as acute renal failure or acute respiratory failure, is documented but the documentation does not link it to the sepsis. In this case, severe sepsis cannot be coded (guideline I.C.1.d.1.a.iv). For instance, if 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.

Coding tips: When severe sepsis is documented, there will be a minimum of two ICD-10-CM codes (guideline I.C.1.d.1.b.). First, code for the underlying systemic infection (i.e., sepsis), followed by a code for severe sepsis (R65.2-). If organ dysfunction other than septic shock is present, add the codes for the specific organ dysfunction.

Septic Shock

Septic shock refers to circulatory failure associated with severe sepsis. It is a life-threatening condition that happens when the exaggerated response to infection leads to dangerously low blood pressure (hypotension). Septic shock is a form of organ failure.

Documentation issues: The term septic shock is occasionally documented without the term sepsis in the chart. If septic shock is documented, A41.9 and R65.21 can be coded. It is important to note that the adjective septic in other instances, such as septic encephalopathy or septic emboli, does not mean that A41.9 can be coded. Follow the Alphabetic Index and the Tabular List for correct coding when the documentation includes the word septic.

Coding tips: According to the guidelines, for all cases of documented septic shock, the code for the underlying systemic infection (i.e., sepsis) should be sequenced first, followed by code R65.21 or T81.12- Post-procedural septic shock. Any additional codes for other acute organ dysfunctions should be reported as well. The code for septic shock R65.21 can never be assigned as the principal diagnosis.

Example: A 90-year-old patient is admitted with septic shock with severe hypotension, tachypnea, and tachycardia. The source is determined to be pneumonia. The patient develops acute hypoxic respiratory failure and acute renal failure, which are documented as related to the sepsis. Correct coding is:

A41.9    Sepsis, unspecified organism


J18.9     Pneumonia, unspecified organism

J96.01   Acute respiratory failure with hypoxia

N17.9    Acute kidney failure, unspecified

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 postoperative wound infections, infusions, transfusions, therapeutic injections, implanted devices, and transplants.

Documentation issues: The physician must document the cause-and-effect relationship between the infection and the procedure or device (guidelines I.B.16 and I.C.1.d.5.a). Common cause-and-effect relational words and phrases include “due to,” “associated with,” “related to,” “attributed to,” and “secondary to.” If the documentation isn’t clear as to the relationship, query the physician. Occasionally, the physician will state “infected PICC line” or “infected spinal hardware.” These are examples of when a cause-and-effect relationship between the implant/device and the infection is implied by the adjective “infected,” and can be coded as a complication.

A query may be necessary when “sepsis due to complicated UTI” is documented on a chart. In this statement, it is unclear what is complicating the UTI. It could be the patient’s medical condition, or it could be an indwelling Foley catheter. It is important that the cause of sepsis be accurately captured because when a complication code is sequenced first, the case will no longer fall under the sepsis MS-DRG and reimbursement will be impacted.

Coding tips: When sepsis is due to a procedural complication, sequence the complication code first, followed by the code for the specific infection. If the patient has severe sepsis, code R65.2- along with the codes for each organ dysfunction. If the exact causative organism is known, code for the infectious agent (guidelines I.C.1.5.b-c).

Obstetrical Sepsis

When sepsis and septic shock are complicating abortion, pregnancy, childbirth, and/or the puerperium, sequence the obstetrical code first, followed by a code for the specific type of infection. Per guideline I.C.15.j, if the patient has severe sepsis, code R65.2- with the codes for each organ dysfunction. Also, if the specific causative organism is known, code for the infectious agent. According to guideline I.C.15.k, code A41.- Other sepsis should not be added for puerperal sepsis.

Guideline I.C.1.d.5.b states that if sepsis occurs due to an obstetric procedure, first assign O86.04 Sepsis following an obstetrical procedure, followed by the codes for sepsis. When documented, report additional codes for severe sepsis and any organ dysfunction.

Newborn Sepsis

When a newborn is diagnosed with sepsis, assign a code from category P36 Bacterial sepsis of newborn. According to guideline I.C.16.f, if a newborn is documented as having sepsis without documentation of whether it is congenital or community-acquired, the default is congenital, and a code from P36 is assigned. Most of the codes in category P36 include the causative organism, so an additional code for the infectious organism should not be assigned. If the P36 code does not identify the specific organism, however, an additional code for the organism can be assigned.

Urosepsis and Sepsis Syndrome

The term urosepsis is no longer indexed in ICD-10-CM. The Alphabetic Index instructs you to “code to condition.” When urosepsis is documented and the patient meets sepsis criteria, the coder must query the physician (guideline I.C.1.d.a.ii).

“Sepsis syndrome” is also not a codable term in ICD-10-CM because it isn’t listed in the Alphabetic Index. The coder must query the provider when the term sepsis syndrome is documented as a final diagnosis and the clinical indicators for sepsis are met.


The definitions of sepsis and the clinical indicators to determine sepsis have changed in Sepsis-3. Per AHA Coding Clinic® (Vol. 3, No. 3, p. 8), regardless of the clinical criteria and definitions that the physicians are using to arrive at a diagnosis of sepsis, code assignment is based on how sepsis is documented. At this time there have been no modifications to the coding guidelines or sepsis coding advice based on these new definitions.

When to Query

Sepsis is a complicated condition to code, and it is often necessary to query the physician to code the case correctly. Consider querying the physician when:

  • Documentation is conflicting, imprecise, incomplete, illegible, ambiguous, or inconsistent
  • Clinical indicators are present without a definitive diagnosis
  • Diagnostic evaluation or treatment was performed without a related diagnosis
  • A diagnosis is made without clinical validation
  • The terms urosepsis or sepsis syndrome are used
  • Severe sepsis is documented without specific organ dysfunctions named
  • Organ dysfunction is not documented as due to sepsis
  • It is unclear whether sepsis was present on admission
  • It’s not clear if the sepsis is related to a device or local infection
  • The patient meets clinical indicators for sepsis and sepsis is only documented by the ED physician or a consulting physician

Make It a Team Effort

To improve sepsis documentation, coding staff needs to work closely with clinical documentation improvement specialists (CDIs), and everyone must be clear on what documentation is needed to correctly code sepsis. A physician champion can be helpful to establish guidelines for the physicians and standard terminology to use when documenting sepsis. A coding tip sheet that includes various scenarios is a helpful tool for the coding department to standardize definitions and the interpretation of the coding guidelines. A regular audit of sepsis DRGs or sepsis as a secondary code can help to identify documentation issues and coders who need more education. Sepsis is never going to be easy to code, but with continuous education and teamwork across departments, the sepsis beast can be conquered.

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