Coding Urinary Tract Infections

Vol. 18 •Issue 9 • Page 10

CCS Prep!

Coding Urinary Tract Infections

Reimbursement and quality regulations require proper coding and reporting of UTIs.

Urinary tract infections (UTI) are a serious health problem affecting millions of people each year. Infections of the urinary tract are the second most common type of infection in the body. Only upper respiratory tract infections (colds and flu) happen more often. According to the Centers for Medicare and Medicaid Services (CMS), catheter-associated UTIs are the most common hospital-acquired infection, accounting for more than 1 million cases in hospitals and nursing homes nationwide. With the implementation of MS-DRG, the importance of coding MCCs and CCs, and the inclusion of catheter-associated UTIs as an initial preventable hospital-acquired condition, correct coding and assignment of UTIs is more important than ever.

A UTI is a bacterial infection of any part of the urinary tract. When bacteria get into the urinary tract and multiply in the urine, they cause a UTI. Predisposing factors for urinary tract infection include calculi or other urinary tract obstruction, foreign bodies such as stents or catheters, congenital urinary anomalies, pregnancy, diabetes mellitus and neurogenic bladder. Women are approximately 10 times more likely to develop a UTI than men.

Physicians often use the term UTI when referring to cystitis, urethritis and pyelonephritis. Lower UTIs include urethritis and cystitis, while pyelonephritis is an upper UTI.

Not all patients have symptoms, but most do have some. Symptoms include dysuria (difficult or painful urination), increased urinary frequency, urgency and often hematuria. Other symptoms include chills, fever, nausea and vomiting, pain and a general feeling of malaise. Each type of UTI may result in more specific signs and symptoms, depending on what is infected.

  • Cystitis is an infection or inflammation of the urinary bladder. Cystitis occurs when the lower urinary tract is infected by bacteria and becomes irritated and inflamed. Symptoms include pelvic pressure, lower abdomen discomfort, frequent, painful urination and cloudy, strong-smelling urine.
  • Pyelonephritis or pyelitis is a urinary tract infection that has spread from the bladder to the kidneys. Kidney infection can cause upper back and flank pain, headache, high fever, shaking chills, and nausea or vomiting. In severe cases, delirium may be present.
  • Urethritis is an infection of the urethra. Symptoms include urethral discharge, dysuria, urgency and increased frequency.

Lab Finding

Urinalysis may show significant bacteriuria, often accompanied by proteinuria, hematuria and pyuria. Urine or catheter culture reveals growth of >100,000 colonies of a single organism. Blood work may reveal neutrophilic leukocytosis and positive blood culture, especially if the infection involves the upper urinary tract. White blood cell shows count of >10,000.

Coding Acute UTIs

One of the most important aspects of coding an acute UTI is documentation of site specificity in the medical record.

  • Acute pyelonephritis: 590.1X, Acute pyelonephritis
  • Acute cystitis: 595.0, Acute cystitis
  • Urethritis: 597.80, Urethritis, unspecified

Code 599.0, Urinary tract infection, site not specified, should be assigned only if the physician has not identified or is unable to identify the site of the UTI.

Code 599.0 should not be used in combination with codes that specifically identify the site of the UTI. For example, if the terms acute cystitis and UTI are both documented separately on the final diagnosis sheet,
only the code for the acute cystitis, 595.0, should be assigned. However, if two specific sites are documented then both should be assigned.

Coding guidelines require the assignment of an additional code if the causative organism is identified. The UTI code is sequenced first, followed by the organism. E. Coli is a common organism causing UTIs and is reported with code 041.4.

Codes from category 599 should not be reported for UTIs in newborns. Code 771.82, Urinary tract infection of newborn, should be assigned instead.

UTI due to Candidal yeast requires one code, 112.2, Candidiasis of other urogenital sites. However, UTI due to noncandidal yeast requires two codes. Code first the appropriate UTI code, followed by 117.9, Other and unspecified mycoses.

UTI and Sepsis

If the documentation indicates that the UTI has progressed to sepsis, code 038.X should be assigned first, then code 995.91, Sepsis, followed by the appropriate UTI code. In this instance sepsis indicates that the UTI has entered the bloodstream and becomes a generalized sepsis. The systemic infection, sepsis, should be sequenced before the localized infection, UTI.


There has been considerable debate in the coding community regarding urosepsis. The term urosepsis is a nonspecific term. The ICD-9-CM Official Guidelines for Coding and Reporting states that if urosepsis is the only term documented, then only code 599.0 should be assigned based on the default for the term in the ICD-9-CM index.

However, often the term urosepsis is used by physicians when in fact the infection has spread to the bloodstream and has progressed to sepsis. The physician should be queried to clarify whether the urosepsis is intended to mean sepsis or UTI. If the physician indicates that the UTI has developed into sepsis, assign the appropriate sepsis codes and then the appropriate UTI code as indicated above.

If urosepsis is meant to mean UTI, then code 599.0 should be assigned along with the causal organism.

Post-operative UTI

If a UTI is diagnosed after a procedure is performed, the coder should not assume that the UTI is a complication of surgery. The physician should be queried.

If the post-operative UTI is linked to the procedure, two codes are required; 997.5, Complications affecting specified body systems, urinary complications, and the appropriate UTI code. If the causative organism is identified it is also coded.

If the physician states that the UTI is not linked to the procedure or is not result of the procedure, then only the appropriate UTI code is assigned.

Foley Catheter Induced UTI

Catheters placed in the urethra and bladder are a common source of UTIs. Often urinary catheters are inserted during surgery. A person who cannot void or who is unconscious or critically ill often needs a catheter that stays in place for a longer period of time. Bacteria on the catheter can infect the bladder, so hospital staff must take special care to keep the catheter clean and remove it as soon as possible.

As indicated earlier, catheter-associated UTIs are the most common hospital-acquired infection, accounting for more than 1 million cases in hospitals and nursing homes nationwide.

According to CMS, it is estimated that hospital-acquired UTIs require one extra hospital day per patient, at an estimated annual cost of $424 to $451 million.

These conditions are reported with code 996.64, Infection and inflammatory reaction due to indwelling urinary catheter, and the appropriate UTI code.

Recurrent and Chronic

Recurrent or chronic UTI without current symptoms should not be coded to the acute infection. Code V13.02, Personal history of urinary (tract) infection, may be assigned to report this. Code V58.62, Long-term (current) use of antibiotics, may also be assigned if the patient is receiving prophylactic antibiotic therapy.


UTIs should not be coded based upon lab results alone. Urine specimens are subject to contamination during collection from microorganisms or by improper handling and storage. Always verify the diagnosis with the physician.

UTI is a commonly missed CC, which may affect MS-DRG assignment. If the medical record contains documentation suggestive of this condition, query the attending physician if it should be added as a secondary diagnosis.

Check yourself on proper coding for UTIs with the quiz below:

1. A patient presents to the ED with a UTI that is due to an indwelling urinary catheter. Which of the following would be the appropriate diagnosis code(s) selection?

a. 996.64, 599.0, E879.6

b. 599.0, 996.64, E879.6

c. 996.64, 599.0

d. 996.64, E879.6

2. Patient with chronic cholecystitis is admitted for an elective cholecystectomy. After admission it was noted by the physician that the patient had developed a UTI based on laboratory tests that were positive for E.Coli. The patient was started on antibiotics, the surgery was cancelled and the patient was discharged. Discharge orders indicate that the surgery was rescheduled in 3 weeks. Which of the following would be the appropriate diagnosis code(s) selection?

a. 599.0, 041.4, 575.11, V64.1

b. 575.11, 599.0, 041.4, V64.1

c. 575.11, 599.0, V64.1

d. 599.0, 575.11, V64.1

3. A patient was discharged following prostate surgery with an indwelling catheter in place. He was readmitted with urinary sepsis due to staphylococcus aureus due to the catheter. The catheter was removed and the patient was started on antibiotic therapy. The patient improved over several days and he was discharged without the indwelling catheter. Which of the following would be the appropriate diagnosis code(s) selection?

a. 996.64, 038.11, 995.91, 599.0, E879.6

b. 038.11, 995.91, 599.0, 996.64, E879.6

c. 996.64, 038.11, 995.91, E879.6

d. 038.11, 995.91, 966.64, E879.6

4. A preterm infant (2,450 grams at birth) was transferred to the current hospital for investigative studies after he was noted to have an elevated temperature and WBCs. A UTI was confirmed with a urine culture that was positive for E. coli. The infection was treated with intravenous antibiotics. Suspected septicemia was ruled out when all blood cultures were negative prior to institution of antibiotic therapy. Which of the following would be the appropriate diagnosis code(s) selection?

a. 599.0, 041.4, 771.82, 765.18, 765.20

b. 771.82, 599.0, 041.4, 765.18, 765.20

c. 771.82, 041.4, 765.18, 765.20

d. 765.18, 771.82, 041.4, 765.20

This month’s column has been prepared by Cheryl D’Amato, RHIT, CCS, director of HIM, facility solutions, Ingenix, and Melinda Stegman, MBA, CCS, clinical technical editor, Ingenix ( Ingenix develops software and e-commerce solutions for managing coding, reimbursement, compliance and denial management in the health care marketplace.

Coding Clinic is published quarterly by the AHA.

CPT is a registered trademark of the AMA.

Answers to CCS PREP!: 1. a: Three codes are reported for this case. Code 996.64 is used to indicate that the infection is due to an indwelling urinary catheter. Code 599.0 is reported to identify the type of infection, UTI, site not specified. Code E879.6 may be reported to indicate that the urinary catheter is the cause of abnormal reaction or later complication; 2. b: The principal diagnosis does not change because the planned procedure was not carried out. Code 575.11, Chronic cholecystitis, is assigned as the principal diagnosis. Codes 599.0 and 041.4 are both assigned to report the UTI due to E.Coli. Code V64.1, Surgical or other procedure not carried out because of contraindications, is assigned to indicate that the procedure was cancelled due to the UTI; 3. a: Code 996.64 is reported as the principal diagnosis to indicate that the sepsis is due to an indwelling urinary catheter. Codes 038.11 and 995.91 are assigned to report the systemic infection, staphylococcus aureus sepsis. Code 599.0 is reported to identify UTI as the localized infection. Code E879.6 may be reported to indicate that the urinary catheter is the cause of abnormal reaction or later complication; and 4. c: Code 771.82 is assigned as the principal diagnosis to report UTI of newborn. Code 041.4 is also assigned to report E. coli as the causative organism. UTI codes from category 599 are excluded for newborns and are not assigned. Code 765.18 is assigned to report the prematurity weighing 2,450 grams at birth. Code 765.20 is required to identify the number of weeks of gestation. In this case, it was unspecified.

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