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Official Description

Infectious agent detection by nucleic acid (DNA or RNA); Clostridium difficile, toxin gene(s), amplified probe technique

© Copyright 2026 American Medical Association. All rights reserved.

Common Language Description

Infectious agent detection by nucleic acid (DNA or RNA) for Clostridium difficile involves identifying the presence of specific toxin genes associated with this bacterium. Clostridium difficile, often referred to as C. difficile, is a significant pathogen that can lead to gastrointestinal issues, primarily diarrhea. While many individuals infected with C. difficile experience mild symptoms that may resolve spontaneously or with antibiotic treatment, the bacterium can also produce potent toxins that damage the intestinal lining, potentially resulting in severe conditions such as colitis or even sepsis. The detection process utilizes advanced molecular techniques, specifically an amplified probe technique, which is crucial for identifying the genetic material of the organism. This method is particularly beneficial when the levels of C. difficile in a specimen are low, as traditional direct probe methods may fail to detect the organism. The amplification process involves replicating specific sequences of DNA or RNA, allowing for enhanced sensitivity in the detection of the pathogen. By employing primers—short strands of DNA or RNA that are designed to bind to the target sequences—the polymerase enzyme can create multiple copies of the desired nucleic acid. Following amplification, a laboratory-prepared probe that is complementary to the C. difficile genetic material is used to confirm the presence of the organism. A successful binding of the probe to the specimen indicates a positive result, often signaled by a color change, thus confirming the presence of C. difficile toxin genes in the sample.

© Copyright 2026 Coding Ahead. All rights reserved.

1. Indications

The procedure for detecting Clostridium difficile toxin genes is indicated in the following scenarios:

  • Diarrhea Patients presenting with diarrhea, particularly when it is severe or persistent, may require testing for C. difficile to determine the underlying cause.
  • Recent Antibiotic Use Individuals who have recently undergone antibiotic treatment are at an increased risk for C. difficile infection, as antibiotics can disrupt normal gut flora, allowing C. difficile to proliferate.
  • Colitis Symptoms Symptoms indicative of colitis, such as abdominal pain, fever, and inflammation of the intestinal lining, warrant testing for the presence of C. difficile toxin genes.
  • Sepsis In cases where a patient exhibits signs of sepsis, particularly with gastrointestinal symptoms, testing for C. difficile may be necessary to rule out or confirm infection.

2. Procedure

The procedure for detecting Clostridium difficile toxin genes using nucleic acid amplification involves several critical steps:

  • Specimen Collection A specimen, typically a stool sample, is collected from the patient. This sample is crucial for the subsequent testing and must be handled according to laboratory protocols to ensure accuracy.
  • Nucleic Acid Extraction The next step involves extracting the nucleic acids (DNA or RNA) from the specimen. This process isolates the genetic material that may contain the target sequences associated with C. difficile.
  • Amplification of Target Sequences Using an enzymatic process, the extracted nucleic acids undergo amplification. Primers that are complementary to the target toxin gene sequences are added, allowing the polymerase enzyme to replicate these specific regions, resulting in an increased quantity of the target DNA or RNA.
  • Probe Hybridization After amplification, a laboratory-prepared probe that is complementary to the C. difficile toxin genes is introduced. This probe binds to the amplified nucleic acids if they are present in the specimen, forming a double-stranded complex.
  • Detection The final step involves detecting the hybridized complex. A change in color or another measurable signal indicates a positive result, confirming the presence of C. difficile toxin genes in the specimen.

3. Post-Procedure

Post-procedure care primarily involves the interpretation of results and subsequent clinical management. If the test result is positive, healthcare providers may initiate appropriate treatment for C. difficile infection, which could include specific antibiotics. It is also essential to monitor the patient for any complications arising from the infection, such as dehydration or severe colitis. In cases of negative results, further evaluation may be necessary to determine the cause of the patient's symptoms. Additionally, proper infection control measures should be implemented to prevent the spread of C. difficile, especially in healthcare settings.

Short Descr C DIFF AMPLIFIED PROBE
Medium Descr INF AGENT DET NUCLEIC ACID CLOSTRIDIUM AMP PROBE
Long Descr Infectious agent detection by nucleic acid (DNA or RNA); Clostridium difficile, toxin gene(s), amplified probe technique
Status Code Statutory Exclusion (from MPFS, may be paid under other methodologies)
Global Days XXX - Global Concept Does Not Apply
PC/TC Indicator (26, TC) 9 - Not Applicable
Multiple Procedures (51) 9 - Concept does not apply.
Bilateral Surgery (50) 9 - Concept does not apply.
Physician Supervisions 09 - Concept does not apply.
Assistant Surgeon (80, 82) 9 - Concept does not apply.
Co-Surgeons (62) 9 - Concept does not apply.
Team Surgery (66) 9 - Concept does not apply.
Diagnostic Imaging Family 99 - Concept Does Not Apply
CLIA Waived (QW) No
APC Status Indicator Conditionally packaged laboratory tests
Type of Service (TOS) 5 - Diagnostic Laboratory
Berenson-Eggers TOS (BETOS) T1H - Lab tests - other (non-Medicare fee schedule)
MUE 2
CCS Clinical Classification 235 - Other Laboratory
90 Reference (outside) laboratory: when laboratory procedures are performed by a party other than the treating or reporting physician or other qualified health care professional, the procedure may be identified by adding modifier 90 to the usual procedure number.
59 Distinct procedural service: under certain circumstances, it may be necessary to indicate that a procedure or service was distinct or independent from other non-e/m services performed on the same day. modifier 59 is used to identify procedures/services, other than e/m services, that are not normally reported together, but are appropriate under the circumstances. documentation must support a different session, different procedure or surgery, different site or organ system, separate incision/excision, separate lesion, or separate injury (or area of injury in extensive injuries) not ordinarily encountered or performed on the same day by the same individual. however, when another already established modifier is appropriate it should be used rather than modifier 59. only if no more descriptive modifier is available, and the use of modifier 59 best explains the circumstances, should modifier 59 be used. note: modifier 59 should not be appended to an e/m service. to report a separate and distinct e/m service with a non-e/m service performed on the same date, see modifier 25.
XU Unusual non-overlapping service, the use of a service that is distinct because it does not overlap usual components of the main service
XS Separate structure, a service that is distinct because it was performed on a separate organ/structure
GW Service not related to the hospice patient's terminal condition
Q4 Service for ordering/referring physician qualifies as a service exemption
GA Waiver of liability statement issued as required by payer policy, individual case
GV Attending physician not employed or paid under arrangement by the patient's hospice provider
26 Professional component: certain procedures are a combination of a physician or other qualified health care professional component and a technical component. when the physician or other qualified health care professional component is reported separately, the service may be identified by adding modifier 26 to the usual procedure number.
76 Repeat procedure or service by same physician or other qualified health care professional: it may be necessary to indicate that a procedure or service was repeated by the same physician or other qualified health care professional subsequent to the original procedure or service. this circumstance may be reported by adding modifier 76 to the repeated procedure or service. note: this modifier should not be appended to an e/m service.
91 Repeat clinical diagnostic laboratory test: in the course of treatment of the patient, it may be necessary to repeat the same laboratory test on the same day to obtain subsequent (multiple) test results. under these circumstances, the laboratory test performed can be identified by its usual procedure number and the addition of modifier 91. note: this modifier may not be used when tests are rerun to confirm initial results; due to testing problems with specimens or equipment; or for any other reason when a normal, one-time, reportable result is all that is required. this modifier may not be used when other code(s) describe a series of test results (eg, glucose tolerance tests, evocative/suppression testing). this modifier may only be used for laboratory test(s) performed more than once on the same day on the same patient.
95 Synchronous telemedicine service rendered via a real-time interactive audio and video telecommunications system: synchronous telemedicine service is defined as a real-time interaction between a physician or other qualified health care professional and a patient who is located at a distant site from the physician or other qualified health care professional. the totality of the communication of information exchanged between the physician or other qualified health care professional and the patient during the course of the synchronous telemedicine service must be of an amount and nature that would be sufficient to meet the key components and/or requirements of the same service when rendered via a face-to-face interaction. modifier 95 may only be appended to the services listed in appendix p. appendix p is the list of cpt codes for services that are typically performed face-to-face, but may be rendered via a real-time (synchronous) interactive audio and video telecommunications system.
GC This service has been performed in part by a resident under the direction of a teaching physician
GY Item or service statutorily excluded, does not meet the definition of any medicare benefit or, for non-medicare insurers, is not a contract benefit
GZ Item or service expected to be denied as not reasonable and necessary
LT Left side (used to identify procedures performed on the left side of the body)
PD Diagnostic or related non diagnostic item or service provided in a wholly owned or operated entity to a patient who is admitted as an inpatient within 3 days
Q1 Routine clinical service provided in a clinical research study that is in an approved clinical research study
QW Clia waived test
RT Right side (used to identify procedures performed on the right side of the body)
SA Nurse practitioner rendering service in collaboration with a physician
X5 Diagnostic services requested by another clinician: for reporting services by a clinician who furnishes care to the patient only as requested by another clinician or subsequent and related services requested by another clinician; this modifier is reported for patient relationships that may not be adequately captured by the above alternative categories; reporting clinician service examples include but are not limited to, the radiologist's interpretation of an imaging study requested by another clinician
XE Separate encounter, a service that is distinct because it occurred during a separate encounter
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2010-01-01 Added -
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