Pneumonia Clinical Indicators, Querying and Coding

MRA Templates (landscape)-Nov-28-2022-03-16-20-5396-PM

A diagnosis of “Pneumonia” in the hospital inpatient setting has seen compliance reviews and Office of Inspector General (OIG) audits dating back to the early 1990s. Now hospitals (facilities) are seeing payer denials for this diagnosis, whether as a Principal diagnosis or as a Secondary (Additional) diagnosis.

Keeping on top of healthcare claim denials can be daunting. For the Health Information Management (HIM) coding professionals and the Clinical Documentation Integrity (CDI) specialists, their expertise can assist and provide insight into solutions and best practices that include clinical indicators, querying and accurate coding.

Pneumonia is an inflammation and/or infection in the air sacs of one or both lungs. Pneumonia can be treated in the outpatient setting or as a hospital inpatient depending on the severity of the symptoms, past medical history and comorbidities. Pneumonia can be caused by a virus (i.e., Respiratory syncytial virus (RSV), SARS-CoV-2 (the virus that causes COVID-19), bacteria (ie., Streptococcus pneumoniae (pneumococcus) and Mycoplasma pneumonia seen especially in children), and fungus (ie., Candidiasis). Pneumonia can also be caused by healthcare-associated setting/encounters,ventilator-associatedd, or associated/caused by aspiration (solids or fluids).

Per the CDC, the following definitions are relevant to inpatient and outpatient coding:

  • Community-acquired pneumonia is when someone develops pneumonia in the community (not in a hospital).
  • Healthcare-associated pneumonia is when someone develops pneumonia during or following a stay in a healthcare setting. Healthcare settings include hospitals, long-term care facilities, and dialysis centers.
  • Ventilator-associated pneumonia is when someone gets pneumonia after being on a mechanical ventilator.

A diagnosis of pneumonia should accompany clinical documentation of the patients signs and symptoms as well as the treatment plan.

Clinical Indicators

“Pneumonia” can have several different clinical indicators, signs and symptoms, including but are not limited to the following:

  • Shortness of breath
  • Wheezing
  • Cough (productive and non-productive)
  • Elevated Temperature
  • Chest Pain
  • Shaking chills
  • Fatigue
  • Abnormal Pulse Oxygen

The above signs and symptoms may be mild or severe, depending on the patients history, presence of comorbidities and prior treatment. The provider may want to conduct the following tests to confirm the diagnosis depending on the severity of the symptoms:

  • X-ray: Chest X-ray is taken to check the presence of infection (sometimes the infiltrate doesn’t appear on the x-ray of the chest due to the patient being dehydrated).
  • Blood culture: To check the presence of infection and identify the causative organism.
  • Sputum culture test: To confirm the cause of infection. (sometimes difficult to obtain a sample)
  • Urine test: Bacterial infection of streptococcus pneumonia and legionella pneumophila can be identified.
  • Pulse oximetry: To measure oxygen flow to the lungs.
  • CT scan: CT scan of chest is performed to detect the severity of infection.
  • Pulmonologist consult and/or Infectious Disease consult
  • Bronchoscopy: A camera fitted tube is inserted into the lungs to look into the airways and to sample out via bronchial wash helping in diagnosing the causative agent.

Identifying the organism responsible for the pneumonia isn’t always easy for the provider and in some cases, it is not identified and the diagnosis will be unspecified pneumonia (ICD-10-CM J18.9). Some bacterial pneumonias do have their own clinical indicators (which will not be discussed in this blog), but are important to be aware of, i.e., color of sputum. Individuals who have Diabetes, Asthma, COPD, or Chronic Heart Disease are at a greater risk of getting Pneumococcal Pneumonia.


Following the AHIMA/ACIDS 2022 Complaint Physician Query will aid both Coding and CDI staff. Having a yes/no query may fit in some situations, but a multiple choice query is the most common and would fit well in clarification of the specific type or organism responsible for the pneumonia.

Here is an example:

Date(query initiated):

Patient Name:                                   Date of Admission:

Provider Name:                                 MR #:

There is documentation in the medical record stating that this patient has a diagnosis of Pneumonia. Please refer to the [Specify where in the medical record: ER documentation & date, Progress Note & date, Pulmonologist Consult & date, etc.].

In addition, please see the [Specify findings and/or treatment: chest x-ray, IV antibiotics XX given, etc.].

Based on your medical judgment, can you further clarify in the progress notes (or the electronic query in the EHR) the most likely or suspected underlying cause of the pneumonia:

[List the different underlying causes that might be responsible for the Pneumonia]

[Include in the choices: Other cause (please specify) • None of the above / Not applicable]

Please exercise your independent professional judgment when responding to this query clarification.

Thank you.

[Name and contact information]


In the ICD-10-CM alphabetic index, there are 112 terms listed under the word Pneumonia. You will find most of the pneumonia codes fall in the tabular Chapter 1 Infectious and Parasitic Diseases or in Chapter 10 Diseases of the Respiratory System.

Coding professionals should conduct a thorough review of the patients history and watch the clinical documentation of “Community-acquired Pneumonia” (CAP), “Hospital-acquired bacterial pneumonia” (HABP) or a diagnosis of “Ventilator-associated bacterial pneumonia” (VABP).

  • Healthcare-associated bacterial pneumonia (also called Hospital-acquired Pneumonia) would be ICD-10-CM code J18.9 Pneumonia, unspecified organism
  • Ventilator-association bacterial pneumonia would be ICD-10-CM code J95.851 Ventilator-associated pneumonia

A research study found that HABP and VABP can be associated with the following common organisms in 80% of episodes:

  • Staphylococcus aureus [28.0%]
  • Pseudomonas aeruginosa [21.8%]
  • Klebsiella species [9.8%]
  • Escherichia coli [6.9%]
  • Acinetobacter species [6.8%]
  • Enterobacter species [6.3%]

Regardless of whether the pneumonia was CAP, HABP or VABP, CDI or Coding professionals should query the physician to determine the pathogen (organism) causing the condition if not documented. Keep a watch out for documentation stating the patient uses/requires oxygen at home, as this would be assigned to “Dependence on supplemental oxygen” with ICD-10-CM code Z99.81).

Having a strong internal process for handling denials requires a “denial committee” or team of healthcare professionals and experts from your hospital. This includes Revenue Cycle, HIM Coding, CDI, Case Management, Patient Financial Services (PFS)/Billing, and a Physician/Provider. There should be a designated leader for denials that can act as a coordinator and help to disseminate the denials that usually come to the PFS department first. This committee or team should have access to data and meet on a regular basis. It’s also a best practice to have a tracking tool for denials and a diagnostic checklist to use when developing the appeal, like when a diagnosis of Pneumonia is denied.

Maintaining and sustaining documentation and coding accuracy is a day-to-day process and it takes dedication, effectiveness, efficiency, communication and compliance. Take a look at your internal processes with regard to the documentation and coding of the diagnosis of pneumonia in your hospital inpatient setting in particular. Remember that we can learn from gaining knowledge of clinical indicators as well as the actual diagnosis denials to identify and implement solutions and improvements. This of course would include conducting some focused audits in the risk and denial area of “Pneumonia” diagnoses. As we head into the winter months we often see an increase in encounters with a diagnosis of Pneumonia, so re-educating now and preparing will help in the long run to decrease denials and improve documentation and coding.


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This program has been approved for continuing education unit(s) (CEUs) for use in fulfilling the continuing education requirements of the American Health Information Management Association (AHIMA). Granting of Approved CEUs from AHIMA does not constitute endorsement of the program content or its program provider.