Test Id : CFRCS

When this test is ordered, the reflex tests may be performed at an additional charge. Antimicrobial agent appropriate to the organism and specimen source will be tested according to Mayo Clinic's practice.

The following tables provide a listing of the antimicrobials routinely tested in the laboratory as well as antimicrobials that may be tested upon request. These tables are organized by isolate groups and are not all inclusive. Call 800-533-1710 and ask to speak to the Bacteriology Antimicrobial Susceptibility Testing Laboratory if the organism or antimicrobial of interest are not listed in these tables.

-Aerobic Gram-Negative Bacilli Antimicrobials 

-Additional Gram-Negative Bacteria Antimicrobials 

-Staphylococcus, Enterococcus, Bacillus, and Related Genera Antimicrobials 

-Additional Gram-Positive Bacteria Antimicrobials

Specimen must be received in laboratory within 48 hours of collection at refrigerated temperature. Specimens received frozen will be rejected.

For shipping information see Infectious Specimen Shipping Guidelines.

Specimen source is required

Submit only 1 of the following specimens:

Preferred:

Specimen Type: Sputum, expectorated or induced

Patient Preparation: Have the patient brush their teeth or gargle with water immediately prior to specimen collection. This reduces the number of contaminating oropharyngeal bacteria.

Container/Tube: Sterile container

Specimen Volume: Entire collection

Acceptable:

Specimen Type: Bronchial aspirate or washing, sinus aspirate, bronchoalveolar lavage, endotracheal, or tracheal

Container/Tube: Sterile container

Specimen Volume: Entire collection

Specimen Type: Throat swab

Supplies:

Culturette (BBL Culture Swab) (T092)

BD E-Swab (T853)

Container/Tube: Culture transport swab (Dacron or rayon swab with aluminum or plastic shaft with either Stuart or Amies liquid medium), or ESwab

Specimen Volume: Entire collection

• Aerobic Gram-Negative Bacilli Antimicrobials
• Additional Gram-Negative Bacteria Antimicrobials
• Staphylococcus, Enterococcus, Bacillus, and Related Genera Antimicrobials
• Additional Gram-Positive Bacteria Antimicrobials

If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.

See Specimen Required

Detecting disease-causing aerobic bacteria in specimens from patients with cystic fibrosis

Determining the in vitro antimicrobial susceptibility of potentially pathogenic aerobic bacteria, if appropriate

When this test is ordered, the reflex tests may be performed at an additional charge. Antimicrobial agent appropriate to the organism and specimen source will be tested according to Mayo Clinic's practice.

The following tables provide a listing of the antimicrobials routinely tested in the laboratory as well as antimicrobials that may be tested upon request. These tables are organized by isolate groups and are not all inclusive. Call 800-533-1710 and ask to speak to the Bacteriology Antimicrobial Susceptibility Testing Laboratory if the organism or antimicrobial of interest are not listed in these tables.

-Aerobic Gram-Negative Bacilli Antimicrobials 

-Additional Gram-Negative Bacteria Antimicrobials 

-Staphylococcus, Enterococcus, Bacillus, and Related Genera Antimicrobials 

-Additional Gram-Positive Bacteria Antimicrobials

Life expectancy of patients with cystic fibrosis (CF) has increased steadily over the past 50 years, in large part due to improvements in the management of lung disease in this patient population. Still, chronic lung infection is responsible for 75% to 85% of deaths in patients with CF. Appropriate treatment for the causative organism can reduce morbidity and mortality.

The number of microbial species associated with CF lung disease is relatively limited. These include Pseudomonas aeruginosa (mucoid and nonmucoid), Staphylococcus aureus, Burkholderia cepacia complex, Stenotrophomonas maltophilia, other non-fermenting gram-negative rods, Haemophilus influenzae, and Streptococcus pneumoniae. Nontuberculous mycobacteria and Aspergillus species may also play a role in CF lung disease, in addition to common respiratory viruses. This culture is specifically designed and utilizes conventional and additional selective media (compared to non-CF respiratory cultures) to isolate bacteria commonly associated with pulmonary disease in patients with CF.

In selected centers, lung transplantation is performed on patients with CF. This test is appropriate for lung transplant patients with underlying CF because they can continue to harbor the same types of organisms as they did pretransplantation. Patients with CF may be colonized or chronically infected by these organisms over a long period of time.

Antimicrobial susceptibility testing determines the minimal inhibitory concentration (MIC) value of selected antimicrobial agents against isolated potentially pathogenic bacteria. The MIC is the lowest antimicrobial concentration (of a series of increasing concentrations) that inhibits growth of the bacterium. Agar dilution MIC testing is performed by testing for growth of bacteria on agar plates containing varying concentrations of antimicrobial agents.

For each organism-antimicrobial agent combination, the Clinical and Laboratory Standards Institute and/or the European Committee on Antimicrobial Susceptibility Testing provide interpretive criteria for determining whether the MIC should be interpreted as susceptible, susceptible-dose dependent, intermediate, nonsusceptible, resistant, or epidemiological cutoff value.

No growth or usual microbiota

Identification of probable pathogens:

Susceptibility results are reported as minimal inhibitory concentration (MIC) in mcg/mL Breakpoints (also known as "clinical breakpoints") are used to categorize an organism as susceptible, susceptible-dose dependent, intermediate, resistant or nonsusceptible according to breakpoint setting organizations, either the Clinical and Laboratory Standards Institute (CLSI) or the European Committee on Antimicrobial Susceptibility Testing (EUCAST), as applicable. In some instances, an interpretive category cannot be provided based on available data and the following comment will be included: "There are no established interpretive guidelines for agents reported without interpretations."

Clinical and Laboratory Standards Institute (CLSI) Interpretive Category Definitions:

Susceptible:

A category defined by a breakpoint that implies that isolates with an MIC at or below or a zone diameter at or above the susceptible breakpoint are inhibited by the usually achievable concentrations of antimicrobial agent when the dosage recommended to treat the site of infection is used, resulting in likely clinical efficacy.

Susceptible-Dose Dependent:

A category defined by a breakpoint that implies that susceptibility of an isolate depends on the dosing regimen that is used in the patient. To achieve levels that are likely to be clinically effective against isolates for which the susceptibility testing results (either MICs or zone diameters) are in the susceptible-dose dependent (SDD) category, it is necessary to use a dosing regimen (ie, higher doses, more frequent doses, or both) that results in higher drug exposure than that achieved with the dose that was used to establish the susceptible breakpoint. Consideration should be given to the maximum literature-supported dosage regimens because higher exposure gives the highest probability of adequate coverage of a SDD isolate. The drug label should be consulted for recommended doses and adjustment for organ function.

Intermediate:

A category defined by a breakpoint that includes isolates with MICs or zone diameters within the intermediate range that approach usually attainable blood and tissue levels and/or for which response rates may be lower than for susceptible isolates.

Note: The intermediate category implies clinical efficacy in body sites where the drugs are physiologically concentrated or when a higher-than-normal dosage of a drug can be used. This category also includes a buffer zone, which should prevent small, uncontrolled, technical factors from causing major discrepancies in interpretations, especially for drugs with narrow pharmacotoxicity margins.

Resistant:

A category defined by a breakpoint that implies that isolates with an MIC at or above or a zone diameter at or below the resistant breakpoint are not inhibited by the usually achievable concentrations of the agent with normal dosage schedules and/or that demonstrate MICs or zone diameters that fall in the range in which specific microbial resistance mechanisms are likely, and clinical efficacy of the agent against the isolate has not been reliably shown in treatment studies.

Nonsusceptible:

A category used for isolates for which only a susceptible breakpoint is designated because of the absence or rare occurrence of resistant strains. Isolates for which the antimicrobial agent MICs are above or the zone diameters are below the value indicated for the susceptible breakpoint should be reported as nonsusceptible.

Note: An isolate that is interpreted as nonsusceptible does not necessarily mean that the isolate has a resistance mechanism. It is possible that isolates with MICs above the susceptible breakpoint that lack resistance mechanisms may be encountered within the wild-type distribution after the time the susceptible-only breakpoint was set.

Epidemiological Cutoff Value:

The MIC that separates microbial populations into those with and without phenotypically detectable resistance (non-wild-type or wild-type, respectively). The epidemiological cutoff value (ECV) defines the highest MIC for the wildtype population of isolates. ECVs are based on in vitro data only, using MIC distributions. ECVs are not clinical breakpoints, and the clinical relevance of ECVs for a particular patient has not yet been identified or approved by CLSI or any regulatory agency.

When an ECV is reported, an interpretive category is not assigned, and the following comment will be included: "This MIC is consistent with the Epidemiological Cutoff Value (ECV) observed in isolates (WITH / WITHOUT) acquired resistance; however, correlation with treatment outcome is unknown."

Wild-type (WT) - an interpretive category defined by an ECV that describes the microbial population with no phenotypically detectable mechanisms of resistance or reduced susceptibility for an antimicrobial agent being evaluated.

Non-wild-type (NWT) - an interpretive category defined by an ECV that describes the microbial population with phenotypically detectable mechanisms of resistance or reduced susceptibility for the antimicrobial agent being evaluated.

Note: MIC values for which ECV's are defined are not to be interpreted or reported as susceptible, intermediate, or resistant but rather as WT or NWT. The ECV's should not be used as clinical breakpoints.(Clinical and Laboratory Standards Institute [CLSI]. Performance Standards for Antimicrobial Susceptibility Testing. 32nd ed. CLSI supplement M100. CLSI; 2022:4-6, 278-279)

European Committee on Antimicrobial Susceptibility Testing (EUCAST) Interpretive Category Definitions:

S - Susceptible, standard dosing regimen: A microorganism is categorized as "Susceptible, standard dosing regimen," when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent

I - Susceptible, increased exposure*: A microorganism is categorized as "Susceptible, Increased exposure*" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.

R - Resistant: A microorganism is categorized as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure*.

*Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

(The European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022;6. Available at www.eucast.org)

A negative test result is no growth of bacteria or growth of only usual microbiota. A negative result does not rule out all causes of infectious lung disease. For more information, see Cautions.

Organisms associated with lower respiratory tract infections are reported.

For positive test results, disease-causing bacteria are identified. Patients with cystic fibrosis may be colonized or chronically infected by some organisms over a long period of time, therefore, positive results must be interpreted in conjunction with previous findings and the clinical picture to appropriately evaluate results.

A susceptible category result and a low minimum inhibitory concentration value indicate in vitro susceptibility of the organism to the antimicrobial tested.

For interpretation of various antimicrobial susceptibility interpretive categories (ie, susceptible, susceptible-dose dependent, intermediate, nonsusceptible, resistant, or epidemiological cutoff value), see Reference Values.

When culture of sputum is delayed, successful isolation of bacterial pathogens is less likely, due to the overgrowth of usual oropharyngeal microbiota.

Some bacterial agents that cause lower respiratory infections (eg, Mycobacteria, Legionella species, Mycoplasma pneumoniae) are not detected by this assay and require special procedures. If the bacterial culture is negative, clinicians should consider additional testing to detect other bacterial, viral, or fungal agents.

Results must be interpreted in conjunction with clinical findings and previous culture results.

When antimicrobial susceptibilities are performed, in vitro antimicrobial susceptibility does not guarantee clinical response. Therefore, the decision to treat with a particular agent should not be based solely on the antimicrobial susceptibility testing result.

1. Miller JM, Binnicker MJ, Campbell S, et al: A guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. 2018 Aug 31;67(6):e1-e94. doi: 10.1093/cid/ciy381

2. York MK, Gilligan P, Alby K: Lower respiratory tract cultures. In: Leber AL, ed. Clinical Microbiology Procedures Handbook, Vol 1, 4th ed. ASM Press; 2016:section 3.11.2

3. LiPuma JJ, Currie BJ, Peacock SJ, VanDamme PAR: Burkholderia, Stenotrophomonas, Ralstonia, Cupriavidus, Pandoraea, Brevundimonas, Comamonas, Delftia, and Acidovorax. In: Carroll KC, Pfaller MC, eds. Manual of Clinical Microbiology. 12th ed. ASM Press; 2019:807-828

• Aerobic Gram-Negative Bacilli Antimicrobials
• Additional Gram-Negative Bacteria Antimicrobials
• Staphylococcus, Enterococcus, Bacillus, and Related Genera Antimicrobials
• Additional Gram-Positive Bacteria Antimicrobials

Standard media (5% sheep blood, chocolate, and eosin methylene blue agar plates) used for respiratory cultures are inoculated. In addition, 2 selective agar plates are utilized to enable isolation of slower growing pathogens that may be easily overgrown by usual microbiota and the longstanding colonization by Pseudomonas aeruginosa. Burkholderia cepacia Selective Agar plate is used for the isolation of B cepacia complex, which includes 20 distinct species. Isolates of B cepacia will be forwarded to the University of Michigan's CFF Research Testing and Repository for genotyping. There is no additional charge for this shipping/testing. A chromogenic Staphylococcus aureus agar is used to enhance the isolation of S. aureus. Finally, a second chocolate blood agar plate is incubated in an anaerobic atmosphere. The anaerobic atmosphere allows for detection of Haemophilus species that may otherwise be overgrown by P. aeruginosa. Pathogens or possible pathogens are identified using 1 or a combination of the following techniques: commercial identification strips or panels, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, conventional biochemical tests, carbon source utilization, real-time polymerase chain reaction, and nucleic acid sequencing of the 16S ribosomal RNA (rRNA) gene.(Gilligan P, Alby K, York MK: Respiratory cultures from cystic fibrosis patients. In: Leber AL, ed. Clinical Microbiology Procedures Handbook, Vol 1, 4th ed. ASM Press; 2016:section 3.11.3)

When antimicrobial susceptibility testing is performed, an agar dilution method is used for routine testing. The agar dilution method employs the use of antimicrobial agents incorporated in agar plates. The antimicrobial is added to agar in various concentrations depending upon levels attainable in serum, urine, or both. A standardized suspension of the organism is applied to the agar plates, which are incubated for a minimum of 16 to 18 hours at 35 degrees C. Complete inhibition of all but one colony or a very fine residual haze represents the end point.(Clinical and Laboratory Standards Institute [CLSI]. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically. 11th ed. CLSI standard M07. CLSI; 2018)

Daptomycin and tigecycline are tested by agar gradient diffusion.(Clinical and Laboratory Standards Institute[CLSI]. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically. 11th ed. CLSI standard M07. CLSI; 2018; package insert: Etest Biomerieux;15203E-EN-2016/07. 07/2016)

 Cefiderocol is tested by disk diffusion.(Clinical and Laboratory Standards Institute [CLSI]. Performance Standards for Antimicrobial Disk Susceptibility Tests. 13th ed. CLSI standard M02.CLSI; 2018)

Monday through Sunday

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• Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
• Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

This test has been cleared, approved, or is exempt by the US Food and Drug Administration and is used per manufacturer's instructions. Performance characteristics were verified by Mayo Clinic in a manner consistent with CLIA requirements.

87070-Bacterial, Culture, cystic fibrosis, respiratory

87077-Identification commercial kit (if appropriate)

87077-Ident by MALDI-TOF mass spec (if appropriate)

87077-Bacteria Identification (if appropriate)

87077-Additional Identification procedure (if appropriate)

87077-Identification Staphylococcus (if appropriate)

87077-Identification Streptococcus (if appropriate)

87147 x 1-3-Serologic agglut method 1 ident (if appropriate)

87147-Serologic agglut method 2 ident (if appropriate)

87147 x 4-Serologic agglut method 3 ident (if appropriate)

87147 x 2-6-Serologic Agglut Method 4 Ident (if appropriate)

87153-Aerobe ident by sequencing (if appropriate)

87150-Identification by PCR (if appropriate)

87185-Beta lactamase (if appropriate)

87186-Antimicrobial Susceptibility, Aerobic Bacteria, MIC-per organism for routine battery (if appropriate)

87181-Susceptibility per drug and per organism for drugs not in routine battery (if appropriate)

87150-mec A PCR (if appropriate)

Sample Reports

Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports

International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports