Cumulative susceptibility data were generated from AST performed at CAHFS. Samples for bacterial culture and AST were from either samples collected and submitted by a client or samples collected by CAHFS’s pathologists from animals received for necropsy. Client information was removed prior to data aggregation. In 2021, approximately 37% of susceptibility tests performed by CAHFS were from client-submitted samples, while 63% were from necropsy samples. Either submitting veterinarians requested AST or CAHFS pathologists provided samples for AST when evidence of disease was found during necropsy and only for submissions listing a reporting veterinarian.
Per CLSI guidelines, samples included in an antibiogram should be associated with disease. Attribution of organisms to disease in the absence of sufficient clinical history or associated lesions at necropsy can be challenging, particularly for organisms that may also be present as commensals (eg, Pasteurella multocida from a nasal swab). Necropsy isolates provided the highest confidence of an organism’s association with disease; those with clinical history gave the next highest confidence. Disease status could not be assessed when clinical history was not provided. Often occurring at other diagnostic laboratories, CAHFS receives a subset of samples without any clinical history but for which AST is requested. As an example, 12% of isolates included in the bovine respiratory disease antibiograms did not have associated data on clinical history, and an additional 4% of isolates were obtained from specimens submitted for routine surveillance. These samples were included in the cumulative susceptibility data, while acknowledging in a disclaimer included with the antibiograms that those samples may have been collected from healthy animals and intended for surveillance purposes.
At the time of publication, CAHFS has released antibiograms for bovine respiratory pathogens (Mannheimia haemolytica, P multocida, and Histophilus somni), ovine and caprine respiratory pathogens (M haemolytica and P multocida), and equine Streptococcus equi subsp zooepidemicus. These were selected on the basis of the availability of adequate isolates (Figure 2) analyzed in a 1-year period and their relative importance to California’s animal industries. Mannheimia spp, Pasteurella spp, and Streptococcus spp are among the most frequent organisms for which AST is performed by CAHFS. In addition, respiratory disease was the third most reported reason for individual animal antimicrobial therapy (bolus/injectable) in cows and replacement heifers and the second most reported reason for similar antimicrobial therapy in calves according to a 2017 survey of California cow-calf operations.7 Respiratory disease therapy was the most reported reason for use of oral and injectable antimicrobials for both ewes and lambs in a 2018 survey of California commercial sheep operations.8 In equine submissions requesting culture and AST at CAHFS, S equi subsp zooepidemicus was one of the most commonly recovered organisms.
Common reasons why bacteria were not included in antibiograms were the following: lack of species-specific breakpoints, insufficient numbers of isolates from a single host species, and recovery from feces or intestinal sites (eg, bovine Salmonella spp), where it is known that the susceptibility of Enterobacterales isolated does not reliably predict the clinical response of treatment for enteric infections.3
Sample processing and analysis
Sample source and clinical history informed CAHFS’s sample processing and culture procedures. Prior to AST, organism identification was verified by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry and biochemical testing methods (Supplementary Material S2).
Approved CLSI breakpoints were used for susceptibility interpretations.4 Where breakpoints were not approved for a specific pathogen-host combination, breakpoints were either extrapolated on the basis of CLSI recommendations or interpretations were not provided.3 When extrapolated, breakpoint source used for interpretations was provided with the antibiogram.
Focus group and expert opinion
A multidisciplinary focus group of California-based large animal clinical veterinarians, academicians, university extensionists, and state-level agriculture and public health veterinarians (n = 16) was recruited to provide guidance on antibiogram design and content. Members were chosen on the basis of their experience with antibiograms, engagement in antimicrobial stewardship programs, and experience with clinical utilization of veterinary medical drugs. Five additional veterinary clinicians at University of California-Davis, selected for their host species expertise, provided feedback on content clarity prior to releasing the final antibiograms.
Veterinarians registered to receive CAHFS livestock antibiograms through an online survey. Promotion of antibiogram availability to veterinarians treating livestock species occurred through social media, newsletters, and veterinary medical associations.
Since 2018, California law has required veterinary oversight for the use of all dosage forms of medically important antimicrobials in livestock6; therefore, access to antibiograms was limited to licensed veterinarians. Respondents were asked to provide a full name, email address, veterinary license number, practice name (if applicable), and the species/production class(es) of interest. If no species/production class was selected, the respondent received all antibiograms. Respondents were required to indicate that they read and understood the following statement: “CAHFS antibiograms are intended for veterinary use only and are not to be distributed to clients/producers without an existing veterinarian-client-patient relationship. It is the veterinarian’s responsibility to use clinical judgment and adhere to label and legal restrictions for use of drugs depicted in CAHFS antibiograms.” Veterinary license numbers were matched to the name using the California Department of Consumer Affairs’ online license search feature to verify the recipient was a veterinarian before sharing the antibiograms.9
To optimize antibiogram utility, the CDFA AUS and CAHFS created educational resources. An outline of laboratory procedures associated with AST, including MIC values and how they relate to antibiograms (Supplementary Figure S2) was published online,10 in addition to a user guide designed to explain the antibiograms, including key formatting and content features.11 Two 1-hour virtual and interactive continuing education sessions were provided through local veterinary medical associations. Sessions described AST from sample collection to interpretation of the MIC report, creation of CAHFS antibiograms, the utility of antibiograms for guiding initial therapy, and limitations of currently available livestock antibiograms.
Enrolled veterinarians received links to the aforementioned published resources, in addition to a digital copy of CLSI’s VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings, First Edition,3 purchased by the CDFA. VET09 contains detailed information to guide AST interpretation and complemented the CDFA AUS’s published outreach.
Antibiogram content and format
The final antibiogram content and format were shaped by CLSI standards and incorporated feedback from the focus group and species experts. Included notations identified where data or methods deviated from CLSI guidelines. Three different formats were created and sent as a PDF to registered veterinarians. The majority opinion from focus group members was that a simple table and bar graph would be useful for quick reference by clinicians but that a detailed table would add valuable information.
A minimum of 30 isolates from a 1-year time span were included for each antibiogram, when possible; if not, the time frame was extended to 2 years, which was noted on the antibiogram for user awareness. When < 30 isolates were available during a 2-year period, a disclaimer was provided indicating that < 30 isolates reduce the statistical validity of the percent susceptible estimates.
Antimicrobial drugs were categorized on the basis of mechanism of action. For host-drug combinations in which drug use is illegal (eg, no fluoroquinolones are licensed in sheep and goats, and extralabel drug use is illegal for fluoroquinolones), susceptibility data were excluded and replaced with a statement that extralabel drug use of that drug is prohibited in the host.5 For drugs that are contraindicated in the host species (eg, tilmicosin in goats), no data were provided and a warning was given not to use the drug in that species. Although CLSI M39 recommends only indicating percent susceptible,2 the intermediate category may predict clinical efficacy in anatomical sites where the drug is known to concentrate or when the dosage may be safely increased.4 Therefore, this information was thought to be useful for clinical decision-making and was included. Furthermore, given inherent variability in test outcomes, inclusion of intermediates was intended to avoid overinterpretation of susceptible or resistant categories.
Up to 3 formats were provided for each host-bacteria combination: a bar chart, a simple table (Figure 3), and a detailed table (Figure 4). The detailed table contained several additional components not found in the simple table, including number and distribution of isolates at each MIC value for the drugs tested. Shading represented the range of antimicrobial concentrations tested, and different colors depicted interpretations of susceptible, intermediate, and resistant, with the darkest color used for resistant. A color palette of light, medium, and dark gold was chosen to enhance visual accessibility. Breakpoints for susceptible, intermediate, and resistant were described for each antimicrobial agent tested. Solid bold lines represented resistant breakpoints along the ranges of antimicrobial concentrations. The distribution of isolates with an MIC at each antimicrobial concentration tested was shown as a percent of the total number included.
The authors thank Drs. Amanda Beaudoin, Barbara Byrne, Terry Lehenbauer, and Virginia Fajt for their valuable review and Megan Harmon for her valuable editing. Thank you to our expert workgroup who guided the direction of California antibiograms.
Antimicrobial stewardship definition and core principles. AVMA. Accessed February 16, 2023. https://www.avma.org/resources-tools/avma-policies/antimicrobial-stewardship-definition-and-core-principles
CVM Guidance for Industry #152: evaluating the safety of antimicrobial new animal drugs with regard to their microbiological effects on bacteria of human health concern. Appendix A: criteria for ranking of antimicrobial drugs according to their importance in human medicine. US FDA. Updated January 27, 2023. Accessed February 16, 2023. https://www.fda.gov/media/69949/download
Livestock: Use of Antimicrobial Drugs. FAC §14400-14408 (2015). https://leginfo.legislature.ca.gov/faces/codes_displayText.xhtml?lawCode=FAC&division=7.&title=&part=&chapter=4.5.&article
AUS Fact Sheets: 2017 Cow Calf Survey. Antibiotic use and stewardship on California’s cow calf operations. California Department of Food and Agriculture. Antimicrobial Use and Stewardship. Accessed February 16, 2023. https://www.cdfa.ca.gov/AHFSS/AUS/docs/AUS_FactSheets_2017CowCalfSurvey.pdf
AUS Fact Sheets: 2018 Commercial Sheep Survey. Antibiotic use and stewardship on California’s sheep operations. California Department of Food and Agriculture. Antimicrobial Use and Stewardship. Accessed February 16, 2023. https://www.cdfa.ca.gov/AHFSS/AUS/docs/AUS_FactSheets_2018SheepSurvey.pdf
California Animal Health and Food Safety Laboratory (CAHFS) antibiogram development process. California Department of Food and Agriculture. Antimicrobial Use and Stewardship. Accessed February 16, 2023. https://www.cdfa.ca.gov/AHFSS/AUS/docs/AntibiogramDevelopment.pdf
California livestock antibiograms: a user guide. California Department of Food and Agriculture. Antimicrobial Use and Stewardship.. University of California-Davis California Animal Health and Food Safety Laboratory. Accessed February 16, 2023. https://www.cdfa.ca.gov/AHFSS/AUS/docs/AntibiogramUserGuide.pdf
Pierce-Hendry SA, Dennis J. Bacterial culture and antibiotic susceptibility testing. Compend Contin Educ Vet. 2010;32(7):E1–E5. Accessed February 16, 2023. https://www.vetfolio.com/learn/article/bacterial-culture-and-antibiotic-susceptibility-testing
CVM Guidance for Industry #263: recommendations for sponsors of medically important antimicrobial drugs approved for use in animals to voluntarily bring under veterinary oversight all products that continue to be available over-the-counter. US FDA. Accessed February 16, 2023. https://www.fda.gov/media/130610/download