Development of a method for creating antibiograms for use in companion animal private practices

Erin Frey 1Departments of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607.

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 DVM, MPH
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Megan Jacob 2Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607.

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Abstract

OBJECTIVE

To identify a method for developing antibiograms for use in companion animal private practices (PPs).

SAMPLES

Reports (n = 532) of aerobic bacterial culture and antimicrobial susceptibility testing performed between January 1, 2018, and December 31, 2018, at 11 PPs and 1 academic primary care practice (APCP).

PROCEDURES

Data extracted from reports included patient identification number, laboratory accession number, patient signalment, collection method, body site, and results of bacterial culture and antimicrobial susceptibility testing. A custom antibiogram was then constructed with the help of commonly available software by adapting methods used by human hospitals. Susceptibility patterns of bacteria isolated by PPs and the APCP were compared to identify challenges associated with collating data from multiple laboratories.

RESULTS

4 bacterial species (Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, and Staphylococcus pseudintermedius) and 3 bacterial groups (Enterobacteriaceae, Enterococcus spp, and coagulase-positive Staphylococcus spp) met the minimum requirement of ≥ 15 isolates for construction of an antibiogram. For urine samples, 3 bacterial species and 2 bacterial groups met the minimum requirement of ≥ 10 isolates. For samples from skin, 2 bacterial species and 2 bacterial groups met the minimum requirement of ≥ 10 isolates. Patient signalment, sample source, and distribution of bacterial isolates were similar between PP and APCP patients.

CONCLUSIONS AND CLINICAL RELEVANCE

Results demonstrated that it was feasible to adapt existing guidelines for developing antibiograms in human medicine to the veterinary outpatient setting. Use of antibiograms could aid in empirical antimicrobial drug selection in a manner that supports antimicrobial stewardship principles.

Abstract

OBJECTIVE

To identify a method for developing antibiograms for use in companion animal private practices (PPs).

SAMPLES

Reports (n = 532) of aerobic bacterial culture and antimicrobial susceptibility testing performed between January 1, 2018, and December 31, 2018, at 11 PPs and 1 academic primary care practice (APCP).

PROCEDURES

Data extracted from reports included patient identification number, laboratory accession number, patient signalment, collection method, body site, and results of bacterial culture and antimicrobial susceptibility testing. A custom antibiogram was then constructed with the help of commonly available software by adapting methods used by human hospitals. Susceptibility patterns of bacteria isolated by PPs and the APCP were compared to identify challenges associated with collating data from multiple laboratories.

RESULTS

4 bacterial species (Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, and Staphylococcus pseudintermedius) and 3 bacterial groups (Enterobacteriaceae, Enterococcus spp, and coagulase-positive Staphylococcus spp) met the minimum requirement of ≥ 15 isolates for construction of an antibiogram. For urine samples, 3 bacterial species and 2 bacterial groups met the minimum requirement of ≥ 10 isolates. For samples from skin, 2 bacterial species and 2 bacterial groups met the minimum requirement of ≥ 10 isolates. Patient signalment, sample source, and distribution of bacterial isolates were similar between PP and APCP patients.

CONCLUSIONS AND CLINICAL RELEVANCE

Results demonstrated that it was feasible to adapt existing guidelines for developing antibiograms in human medicine to the veterinary outpatient setting. Use of antibiograms could aid in empirical antimicrobial drug selection in a manner that supports antimicrobial stewardship principles.

Antimicrobial-resistant bacterial infections are becoming a daily concern for veterinarians and threaten the health and welfare of patients and their caregivers. To address the increase in antimicrobial resistance and preserve the effectiveness and availability of antimicrobials, professional organizations have outlined core principles and actions that promote the judicious use of antimicrobials and define veterinarians’ roles in antimicrobial stewardship.1–5 In addition, consensus groups such as ISCAID have published guidelines to educate veterinarians and provide tools that support the principles of antimicrobial stewardship.6–8

One of the basic principles of antimicrobial stewardship is to promote laboratory testing, including AST, to aid in selecting appropriate antimicrobials. Unfortunately, a 2015 survey9 of AVMA members found that 84% of respondents felt that the cost of bacterial culture and AST prevented them from recommending these to clients. Although the true percentage of patients prescribed antimicrobials that also had AST performed is unknown, sporadic reports suggest that this percentage is low. For example, a Canadian study10 of companion animal veterinarians found that AST was performed in only 4% of cases in which antimicrobials were prescribed.

Even when samples are submitted for bacterial culture and AST, the lag time before results are received leaves a gap when practitioners must make empirical choices about antimicrobial administration. In these instances, antibiograms have been promoted as a tool to improve empirical antimicrobial selection.3,11 The CLSI defines an antibiogram or “cumulative AST data summary” as “the report generated by analysis of results on isolates from a particular institution(s) in a defined period of time that reflects the percentage of first isolates (per patient) of a given species that is susceptible to each of the antimicrobial agents routinely tested.”12 To improve validity, only data for the same patient population for which the antibiogram will be used should be included. To reduce bias associated with recurrent and refractory infections, only data for the first occurrence of a bacterial species isolated from any patient should be included. Finally, to ensure currency and evaluation of trends, data should be confined to a defined period (eg, 1 year) and updated annually.

A CLSI consensus committee of subject matter experts in microbiology, pharmacology, and public health has developed a standardized method for constructing antibiograms.12 This committee's efforts were focused on human medicine, and as of this time, there is not a similar document published for veterinary medicine. Currently, clinical microbiology laboratories in human hospitals create custom antibiograms for their patient populations, but these institutions have the benefit of large patient populations and dedicated microbiology laboratories that comply with CLSI standards. Some veterinary teaching hospitals have also created antibiograms for their patient populations, but the bacterial species and antimicrobial susceptibility profiles for isolates from patients treated at tertiary care veterinary teaching hospitals would not be expected to reflect findings for isolates from patients treated at surrounding primary care PPs.

The objective of the study reported here was to identify a method for developing antibiograms that companion animal PPs could use to assist in empirical selection of antimicrobial treatments for their own patient populations. The method studied was adapted from CLSI guidelines developed for use by human hospitals.12 As secondary objectives, we wanted to determine whether an antibiogram developed on the basis of data for the patient population of an APCP would be representative of antibiograms developed on the basis of data for surrounding companion animal PPs and whether AST data from multiple clinical microbiology laboratories could be combined when creating regional antibiograms.

Materials and Methods

Recruitment of participating PPs

To fulfill the study objectives, data were needed from multiple PPs of various sizes and locales (ie, urban, suburban, and rural) that were located in the general region around an APCP in North Carolina. Therefore, the medical director of a group of 19 privately owned companion animal practices located in central and eastern North Carolina was contacted and agreed to provide access to AST reports for January 1, 2018, through December 31, 2018. Data collection was limited to reports from primary care, or first opinion, practices that all submitted their patient samples to the same commercial laboratory for bacterial culture and AST. Other practice types (eg, emergency and referral hospitals and spay and neuter clinics) in the practice group were excluded because of concerns that testing and antimicrobial use practices at these practices might not reflect those of primary care PPs. The likelihood of this differential behavior was inferred from findings for human medicine, for which antimicrobial prescribing behavior has been found to vary by provider type (eg, urgent care clinics, emergency departments, retail clinics, and traditional ambulatory care offices).13

Data collection

To compile AST data for participating companion animal PPs, practice managers were asked to generate lists of patients with billing codes for aerobic bacterial culture and urine culture during the study period. On the basis of patient identification numbers and dates of sample submission from these lists, AST reports were located on the commercial laboratory's website. To capture additional episodes of bacterial culture that had been performed but may not have been billed, the web-based laboratory database was searched with the keywords “culture” and the names of all veterinarians included in the billing code list from each practice. Any AST reports not previously identified were included in the study.

Similarly, a query of the university hospital billing system was performed to generate a list of patients of the APCP with the billing code for aerobic bacterial culture. This list was then crossmatched with AST reports from the on-site clinical microbiology laboratory. Results of AST for samples billed but not reported in the query of the laboratory database were added manually by consulting patient files in the hospital electronic medical records system. Data were excluded if samples had been obtained from any species other than dogs and cats or if only anaerobic or fungal culture had been performed.

Data from the PPs and APCP were uploaded into a spreadsheet program. Variables reported for each culture event represented a relevant subset of those described in the CLSI reference document for constructing antibiograms adapted to the veterinary medical setting12 (Appendix). To ensure individual identification of each culture event, a unique patient identification number from the practice record along with personal identifiers (ie, patient name, age, sex, and species and client last name) were included. Each culture event was identified with a unique laboratory accession number and submission date to facilitate identification of the first occurrence of a bacterial isolate from a particular body site for each patient. When a single patient sample had mixed bacterial growth (ie, > 1 bacterial type, including multiple biotypes of the same bacterial species), each isolate was recorded as a separate line entry.

Body site categories corresponded with CLSI guidelines for establishing antimicrobial drug breakpoints.14 Categories consisted of urine (including bladder wall), skin (including anatomic sites on the skin such as axilla, digit, draining tract, ear, incision site, paw, skin scrape, and toe), abscess or wound, genital tract (including uterus), respiratory tract (including nasal cavity), and soft tissue (including kidney, liver, and abdomen). Samples not aligning with these body categories were labeled as “other” (eg, anal gland, fluid, and lip). For urine samples, the method of collection (eg, free catch, cystocentesis, or catheterization) and number of CFUs/mL were extracted from the electronic medical record and AST report, respectively, to determine whether bacterial growth was clinically relevant or likely a contaminant.

For each antimicrobial drug reported, the MIC and interpretation (susceptible, intermediate, or resistant) were recorded. Although both microbiology laboratories from which data were obtained used standard CLSI breakpoints for determining whether a bacterial isolate was susceptible to each antimicrobial drug, MICs were included to facilitate comparisons resulting from differences in MIC testing platformsa,b between laboratories and updated CLSI breakpoints from 2018.14,15

Epidemiological analysis

To evaluate whether the APCP patient population for which samples had been submitted for bacterial culture was representative of the PP patient population, descriptive characteristics of patients for which at least 1 sample had been submitted for aerobic bacterial culture were compared. Factors considered consisted of age (median, range, and interquartile [25th to 75th percentile] range), species (canine vs feline), and sex (male vs female). Reproductive status was not considered owing to a lack of data in the laboratory reports regarding whether patients were spayed or neutered.

Comparisons were repeated for patients that had clinically relevant growth on AST reports to determine whether antibiograms developed for common patient site and bacteria combinations (eg, urine and Escherichia coli or skin and Staphylococcus pseudintermedius) would be comparable between PPs and the APCP. Samples for which no growth, growth of mixed flora only, growth of normal flora only, or growth only in thioglycolate broth was reported were removed because of a subjective assessment of lack of clinical relevance. The term mixed flora was used by the commercial laboratory when ≥ 2 organisms with low growth (< 1,000 CFUs/mL) were isolated from urine. Because urinary tract infections are typically caused by a single pathogen,16 this was considered an overgrowth of contaminants by the commercial laboratory. Bacteria isolated from free-catch urine samples at concentrations < 10,000 CFUs/mL were not considered clinically relevant.17 When > 1 sample was submitted in a single day from the same site for a single patient, results for only 1 sample were included. For example, if a swab sample from the skin surface and a punch biopsy sample of the skin from the same patient were both submitted, results for only the punch biopsy sample were included because they were considered more clinically relevant.

Developing a list of clinically relevant bacteria

After results of bacterial culture that did not meet the criteria for inclusion were removed, a list of bacteria sorted by species and genus was developed. In some instances, the laboratory did not perform AST for certain species of bacteria. For example, AST was typically not performed for bacteria considered by the laboratory to be environmental contaminants or commensal organisms unlikely to be pathogenic (eg, Acinetobacter spp, nonhemolytic Streptococcus spp, and Serratia marcescens isolated from urine), bacteria for which CLSI interpretive guidelines were not available (eg, Actinomyces spp, Bacillus spp, and Corynebacterium spp), bacteria for which the effectiveness of recommended antimicrobials was deemed by the laboratory to be predictable for that species (eg, β-hemolytic Streptococcus spp and Pasturella multocida), bacteria known to have intrinsic resistance to many antimicrobial drugs and for which AST results were considered unlikely to be predictive of a clinical response (eg, Stenotrophomonas maltophila), and bacteria for which AST was not routinely performed for other reasons (eg, Nocardia spp).

Although CLSI guidelines12 suggest that bacterial species be included in an antibiogram only if results of AST are available for a minimum of 30 isolates, we elected to include bacterial species for which results of AST were available for a minimum of 15 isolates. In some instances when individual bacterial species did not meet this threshold, data from multiple species were combined. These included Enterobacteriaceae (E coli, Klebsiella pneumoniae, Proteus mirabilis, Citrobacter braakii, and Citrobacter freundii), the coagulase-positive Staphylococcus group (Staphylococcus aureus, Staphylococcus intermedius, S pseudintermedius, Staphylococcus schleiferi, and coagulase-positive, hemolytic Staphylococcus spp), and the Enterococcus group (Enterococcus avium, Enterococcus casseliflavus, Enterococcus faecalis, and Enterococcus gallinarum). Enterococcus faecium was not included in the Enterococcus group because its resistance profile is known to be different from that of other Enterococcus spp, with E faecium typically more likely to be resistant. In instances when ≥ 10 isolates were obtained from a single body site category (eg, urine or skin), an antibiogram was also developed for isolates from that site.

Suppressed and supplemental AST results

Although CLSI recommends reporting susceptibility for all antimicrobials for which a bacterial isolate is tested, laboratories may have algorithms to suppress susceptibility results for certain antimicrobials (eg, imipenem or vancomycin) or to perform supplemental AST for isolates with multidrug resistance. Reporting algorithms were not known for the 2 laboratories participating in the study; however, personnel in the microbiology laboratory used by the APCP were able to provide suppressed AST data for certain antimicrobial drugs for Staphylococcus isolates to allow comparisons between PP and APCP samples.

Summary antibiogram

For each bacterial species and bacterial group that met the threshold for minimum number of isolates, median MIC and percentage of isolates classified as susceptible were calculated with standard software.c Antibiograms were then created on the basis of all bacteria isolated from any body site and on the basis of bacteria isolated from specific body site categories because it was thought that antibiograms developed on the basis of these body site–bacterial species combinations would be of greater clinical relevance.8,16,18 Body site–specific tables were organized according to ISCAID consensus guidelines for the treatment of sporadic bacterial cystitis in dogs and cats and superficial bacterial folliculitis in dogs.6,8

Comparing antibiograms between PPs and the APCP

To evaluate the feasibility of combining sample results from different microbiology laboratories, a comparative antibiogram was built for a common bacterial species and body site combination (E coli from urine). A similar comparison of S pseudintermedius isolates from skin was not performed owing to the small number of isolates from the APCP.

Statistical analysis

Descriptive characteristics of patients and body site categories of samples were compared between the PPs and APCP with a χ2 testc or Fisher exact test (for comparisons with an expected value < 5 in any cell).d Values of P < 0.05 were considered significant.

Results

Characteristics of patients and samples

Eleven PPs located in 7 counties in central and eastern North Carolina were included in the study. Five of the 7 counties where the 11 PPs were located were contiguous with each other, and the geographic center of these counties, Wake County, was the county in which the APCP was located. A total of 428 samples from 350 PP patients and 104 samples from 78 APCP patients were submitted for culture and AST during the study period of January 1, 2018, through December 31, 2018 (Table 1; Figure 1). This represented 0.1% to 1% of PP patient visits and 4% of APCP patient visits. For the 11 PPs, number of samples submitted ranged from 1 to 146; 4 of the PPs submitted 338 of the 428 (79%) samples.

Table 1—

Characteristics of bacterial culture and AST results for samples submitted between January 1, 2018, and December 31, 2018, by 11 PPs and an APCP in North Carolina; results were subsequently used in developing antibiograms.

 All samples Samples with clinically relevant growth 
VariablePPsAPCPP value*PPsAPCPP value*
No. of samples428104 22647 
Body site category  0.05  0.11
  Urine315 (74)86 (83) 130 (58)33 (70) 
  Any other site113 (26)18 (17) 96 (42)14 (30) 
No. of patients35078 19937 
Age (y)9 (6–13)11 (6–14) 10 (6–12)11 (5–13) 
Species  < 0.01  < 0.01
  Canine286 (82)47 (60) 181 (91)26 (70) 
  Feline64 (18)31 (40) 18 (9)11 (30) 
Sex  0.81  0.47
  Male134 (38)31 (40) 77 (39)12 (32) 
  Female216 (62)47 (60) 122 (61)25 (68) 

P values represent results of a χ2 or Fisher exact test for an association between practice type (PPs vs APCP) and the variable of interest.

Data represent number (percentage) for each practice type.

Data represent median (interquartile [25th to 75th percentile] range).

Figure 1—
Figure 1—

Flow diagrams illustrating identification of bacterial culture and AST results for samples submitted between January 1, 2018, and December 31, 2018, by 11 PPs and an APCP in North Carolina; results were subsequently used in developing antibiograms.

Citation: Journal of the American Veterinary Medical Association 257, 9; 10.2460/javma.257.9.950

The most common body site category for samples was urine (315/428 [74%] for PPs and 86/104 [83%] for the APCP), followed by skin (68/428 [16%] for PPs and 14/104 [13%] for the APCP). More samples were obtained from dogs than from cats. When considering all patients for which samples were submitted for culture and AST, there was a significant association between species (canine vs feline) and practice type (PP vs APCP; P < 0.01), but not between sex (male vs female) and practice type (P = 0.81; Table 1).

Percentages of samples that yielded clinically relevant growth were not significantly (P = 0.16) different between the PPs (226/428 [53%]) and the APCP (47/104 [45%]; Table 1). For samples that yielded clinically relevant growth, body site category (urine category vs all nonurine categories) was not significantly (P = 0.11) associated with practice type (PP vs APCP). For patients from which samples with clinically relevant growth were obtained, species (canine vs feline; P < 0.01), but not sex (male vs female; P = 0.47), was significantly associated with practice type. In addition, for patients from which urine samples with clinically relevant growth were obtained, species (canine vs feline; P < 0.01), but not sex (male vs female; P = 0.55), was significantly associated with practice type (Table 2). However, for patients from which samples other than urine with clinically relevant growth were obtained, neither species (canine vs feline; P = 0.39) nor sex (male vs female; P = 0.50) was significantly associated with practice type.

Table 2—

Characteristics of patients in Table 1 from which samples with clinically relevant bacterial growth were obtained, stratified on the basis of body site category.

 Urine All other sites 
VariablePPsAPCPP value*PPsAPCPP value*
No. of patients111 (56)28 (76) 88 (44)9 (24)0.08
Age (y)11 (9–13)12 (8–14) 7 (4–11)5 (4–9) 
Species  < 0.01  0.39
  Canine97 (87)18 (64) 84 (95)8 (89) 
  Feline14 (13)10 (36) 4 (5)1 (11) 
Sex  0.55  0.50
  Male30 (27)6 (21) 47 (53)6 (67) 
  Female81 (73)22 (79) 41 (47)3 (33) 

The urine category consisted of urine and bladder wall samples.

See Table 1 for key.

Characteristics of clinically relevant bacterial growth

A total of 451 isolates were obtained from the 273 samples with bacterial growth. However, 60 of these isolates were excluded from consideration because they were classified as environmental contaminants or commensal organisms or because AST was not performed. Of the remaining 391 isolates, 333 were from PPs and 58 were from the APCP.

Four bacterial species (E coli, P mirabilis, Pseudomonas aeruginosa, and S pseudintermedius) and 3 bacterial groups (Enterobacteriaceae, Enterococcus group, and coagulase-positive Staphylococcus group) met the minimum requirement for inclusion in an antibiogram of ≥ 15 isolates (Table 3). For urine samples, 3 bacterial species (E coli, P mirabilis, and S pseudintermedius) and 2 bacterial groups (Enterobacteriaceae and Enterococcus group) met the minimum requirement of ≥ 10 isolates (Table 4). For samples from skin, 2 bacterial species (P aeruginosa and S pseudintermedius) and 2 bacterial groups (Enterobacteriaceae and coagulase-positive Staphylococcus group) met the minimum requirement of ≥ 10 isolates (Table 5).

Table 3—

Classification of bacterial isolates obtained from the PPs (n = 333 isolates) and APCP (58 isolates) described in Table 1 (only bacterial species or groups with ≥ 15 isolates are listed).

Bacterial group and speciesPPsAPCP
Enterobacteriaceae*120 (36)22 (38)
  Citrobacter brakii10
  Citrobacter freundii10
  Escherichia coli7421
  Klebsiella sp80
  Proteus mirabilis361
Enterococcus group*32 (10)7 (12)
  Enterococcus avium01
  Enterococcus casseliflavus10
  Enterococcus faecalis224
  Enterococcus gallinarum10
  Enterococcus sp82
Coagulase-positive Staphylococcus group*64 (19)11 (19)
  Coagulase-positive Staphylococcus sp11
  Staphylococcus aureus20
  Staphylococcus pseudintermedius519
  Staphylococcus schleiferi101
Pseudomonas aeruginosa*19 (6)2 (3)

Data represent number (percentage) of isolates for that practice type.

Table 4—

Representative antibiogram for urine and bladder wall samples submitted for bacterial culture and AST by the PPs and APCP described in Table 1.

 Gram negativeGram positive
AntimicrobialE coliP mirabilisEnterobacteriaceaeEnterococcus groupS pseudintermedius
No. of isolates5124821910
First-line choices*     
  Amoxicillin61% (8)75% (2)60% (4)84% (NR)40% (NR)
  Amoxicillin–clavulanic acid71% (4)96% (4)78% (2)94% (2)100% (2)
  Trimethoprim-sulfamethoxazole90% (20)96% (20)93% (20)IR80% (10)
Second-line choices*     
  Cefovecin80% (1)96% (0.5)85% (0.5)IR100% (0.5)
  Enrofloxacin86% (0.12)100% (0.12)91% (0.12)47% (0.5–1)90% (0.5)
  Marbofloxacin88% (0.5)100% (0.5)93% (0.5)47% (2)90% (0.5)
Other choices based on AST results     
  Amikacin98% (2)100% (2)99% (2)IR100% (2)
  Cefotaxime88% (NR)100% (NR)93% (NR)IRNI
  Cefpodoxime78% (0.25)100% (0.25)85% (0.25)IR100% (0.5)
  Ceftazidime84% (0.12)100% (0.12)90% (0.12)IRNI
  Ceftiofur80% (1)100% (1)87% (1)IRNI
  Cephalexin71% (8)25% (16)56% (8)IR100% (2)
  Chloramphenicol53% (8)75% (4–8)62% (8)89% (4–8)80% (8)
  Ciprofloxacin88% (0.06)100% (0.06)93% (0.06)47% (NR)90% (NR)
  ClindamycinIRIRIRIR70% (0.25)
  Doxycycline83% (1)0% (16)69% (1–2)58% (0.5)NS
  Gentamicin96% (1)96% (1)96% (1)IR90% (0.5)
  Imipenem98% (1)NSNSNI100% (NR)
  MinocyclineNINININI67% (0.5)
  Nitrofurantoin98% (16)0% (128)§63% (16)100% (16)100% (16)
  OxacillinNINININI100% (0.25)
  PenicillinNINININI30% (0.5)
  Piperacillin68% (4)88% (4)72% (4)NINI
  Rifampin||IRIRIRNI100% (0.5)
  Tetracycline93% (1)0% (16)§60% (1)67% (1)57% (2)

Data represent percentage of tested isolates with an interpretation of susceptible (median MIC [μg/mL]). Bold numbers indicate susceptibility results were available for all bacterial isolates.

Antimicrobials designated in the ISCAID consensus guidelines8 as first- and second-line choices for the treatment of sporadic bacterial cystitis in dogs.

Susceptibility interpretive breakpoint was changed by CLSI in 2018.14

Use of ciprofloxacin in dogs and cats is not recommended because variability between patients in how the drug is absorbed, distributed, and metabolized means that blood and tissue concentrations are unpredictable.19–22

According to CLSI guidelines,14 P mirabilis demonstrates intrinsic resistance to nitrofurantoin and tetracycline.

Rifampin is tested as a supplemental antimicrobial for treatment of methicillin-resistant Staphylococcus spp and is not recommended for routine use.

IR = Antimicrobial is not expected to be effective clinically because of intrinsic resistance of isolates.14 NI = Antimicrobial was not included on report of AST results. NR = MIC was not reported. NS = Data were not sufficient (ie, ≤ 5 isolates were tested for susceptibility to this antimicrobial).

Table 5—

Representative antibiogram for skin samples (including anatomic sites on the skin such as axilla, digit, draining tract, ear, incision site, paw, skin scrape, and toe) submitted for bacterial culture and AST by the PPs and APCP described in Table 1.

 Gram negativeGram positive
AntimicrobialEnterobacteriaceaeP aeruginosaS pseudintermediusCoagulase-positive Staphylococcus group
No. of isolates16113142
First-line choices*    
  Amoxicillin–clavulanic acid88% (2)IR61% (2)62% (2)
  Cephalexin38% (16)IR61% (2)62% (2)
  ClindamycinIRIR55% (0.25)64% (0.25)
  Trimethoprim-sulfamethoxazole94% (20)IR58% (10)69% (10)
Other choices based on AST results    
  Amikacin100% (2)64% (2)97% (2)98% (2)
  Amoxicillin81% (4)IR10% (NR)24% (NR)
  AzithromycinIRIR52% (NR)62% (NR)
  Cefotaxime88% (NR)IRNINI
  Cefovecin88% (0.5)IR61% (0.5)62% (0.5)
  Cefpodoxime88% (0.25)IR61% (0.5)62% (0.5)
  Ceftazidime88% (0.12)86% (2)NINI
  Ceftiofur75% (1)NININI
  Chloramphenicol69% (8)9% (64)100% (8)100% (8)
  Ciprofloxacin94% (0.06)91% (0.25–0.5)65% (NR)62% (NR)
  Doxycycline58% (1)IR47% (1)59% (0.5)
  Enrofloxacin94% (0.12)18% (1)55% (0.5)55% (0.5)
  ErythromycinIRIR52% (0.5)62% (0.25)
  Gentamicin94% (1)91% (1)68% (0.5)74% (0.5)
  Imipenem100% (0.25)100% (2)61% (NR)62% (NR)
  Marbofloxacin94% (0.5)82% (0.5)61% (1)60% (0.5)
  MinocyclineNIIR87% (0.5)90% (0.5)
  OxacillinNIIR61% (0.25)62% (0.25)
  PenicillinNIIR10% (0.5)24% (0.5)
  Rifampin||IRIR100% (0.5)96% (0.5)
  TetracyclineNSIR57% (1)70% (1)

Data represent percentage of tested isolates with an interpretation of susceptible (median MIC [μg/mL]). Bold numbers indicate susceptibility results were available for all bacterial isolates.

Antimicrobials designated in the ISCAID consensus guidelines6 as first-line choices for the treatment of superficial bacterial folliculitis in dogs.

See Table 4 for remainder of key.

Eight patients had > 1 bacterial isolate from a single bacterial group. This included 7 patients with 2 isolates each in the Enterobacteriaceae group (E coli and P mirabilis, n = 5; E coli and C freundii, 1; and E coli and K pneumoniae, 1) and 1 patient with 2 isolates in the coagulase-positive Staphylococcus group (S pseudintermedius and S schleiferi). In these instances, both isolates were included in the antibiogram.

Comparison of antibiograms between PPs and the APCP

The AST platformsa,b used by the PPs and the APCP yielded slightly different antimicrobial susceptibility reports. However, in those instances when direct comparisons between practice types could not be made, comparisons of drugs within the same drug class were possible. The greatest difference between the PP and APCP antibiograms for E coli isolates from urine was the percentage susceptibility for amoxicillin–clavulanic acid (71% [PP] vs 100% [APCP]) and chloramphenicol (53% [PP] vs 89% [APCP]; Table 6).

Table 6—

Comparative antibiograms for E coli isolates from urine and bladder wall samples submitted for bacterial culture and AST by the PPs and APCP in Table 1.

AntimicrobialPPsAPCP
No. of isolates5119
Initial choices*  
  Amoxicillin61% (8)NI
  Amoxicillin–clavulanic acid71% (4)100% (4)
  Trimethoprim-sulfamethoxazole90% (20)100% (0.5)
Second-line choices*  
  Enrofloxacin86% (0.12)100% (0.12)
  Marbofloxacin88% (0.5)100% (0.12)
  Cefovecin80% (1)92% (1)
Other choices based on AST results  
  Cephalexin71% (8)71% (8)
  CefazolinNI74% (2)
  Cefpodoxime78% (0.25)84% (1)
  OrbifloxacinNI94% (1)
  PradofloxacinNI100% (0.25)
  Doxycycline83% (1)95% (1)
  Tetracycline93% (1)88% (4)
  Amikacin98% (2)100% (4)
  Gentamicin96% (1)95% (0.5)
  Chloramphenicol53% (8)89% (8)
  Nitrofurantoin98% (16)NI
Not recommended  
  Ciprofloxacin88% (0.06)NI
  Imipenem98% (1)NS

Data represent percentage of tested isolates with an interpretation of susceptible (median MIC [μg/mL]). Bold numbers indicate susceptibility results were available for all bacterial isolates.

Antimicrobials designated in the ISCAID consensus guidelines8 as first- and second-line choices for the treatment of sporadic bacterial cystitis in dogs.

See Table 4 for remainder of key.

Discussion

Results of the present study demonstrated that it was feasible to adapt existing guidelines12 for developing antibiograms in human medicine to the veterinary outpatient setting. The most challenging aspect of constructing antibiograms in the present study was meeting the threshold of ≥ 30 isolates of each bacterial species. Even when starting with culture and AST results for 428 samples collected by 11 PPs and an APCP over a 1-year period, only 3 bacterial species (E coli, P mirabilis, and S pseudintermedius) met that threshold. Therefore, we elected to decrease the threshold to 15 isolates for the purposes of the present study. In addition, to enhance the clinical relevance of the antibiograms while minimizing bias associated with small sample sizes, we grouped several bacterial species into larger groups. Our findings emphasized the importance of submitting patient samples for bacterial culture and AST. Also, the fact that only 4 practices submitted 79% (338/428) of the samples suggested that smaller numbers of PPs could be used to develop antibiograms if the volume of testing in each clinic was sufficient.

Although our goal in the present study was to include only the first isolate of any bacterial species for each patient, there were instances when multiple isolates of the same bacterial genus were recovered from a single patient on the same day. In these instances, we used results for the isolate identified to the species level, the isolate known to be pathogenic (vs commensal), or the most resistant isolate. Thus, for example, we included results for E faecalis (identified to the species level and known to be pathogenic) over results for Enterococcus sp and included results for S pseudintermedius (known to be pathogenic) over results for S epidermidis (considered to be commensal). One exception to this convention was when considering bacterial groups (ie, Enterobacteriaceae, coagulase-positive Staphylococcus group, and Enterococcus group). In these instances, if ≥ 2 bacterial species were recovered from an individual patient (eg, both E coli and P mirabilis isolated from a urine sample), results for both isolates were included.

For the antibiogram constructed for bacterial isolates from urine samples, there were insufficient MIC data (ie, ≤ 5 isolates) to report percentage susceptible to pradofloxacin, azithromycin, and erythromycin for S pseudintermedius isolates. For the antibiogram constructed for bacterial isolates from skin samples, there were insufficient MIC data to report percentage susceptible to pradofloxacin for S pseudintermedius isolates or percentage susceptible to piperacillin and tobramycin for Enterobacteriaceae and P aeruginosa isolates. Although topical antimicrobial drugs were included on AST reports, they were not included in the antibiogram because currently there are no CLSI breakpoint interpretations for topical regimens, and breakpoints based on systemic formulations should not be applied to topical regimens.19 Despite the high reported susceptibility to ciprofloxacin in our antibiograms, the use of ciprofloxacin in dogs and cats is not recommended because variable drug absorption, distribution, and metabolism lead to unpredictable blood and tissue concentrations of the drug in these patients.19–22 If a fluoroquinolone is indicated, preference should be given to drugs labeled for use in dogs and cats.6 Similarly, although included in the antibiogram, rifampin susceptibility was reported only as supplemental testing for methicillin-resistant Staphylococcus spp, and its use is only recommended for isolates with multidrug resistance and supportive AST findings.6

Stratifying antibiograms by body site in the present study allowed application of ISCAID's disease-specific guidelines to the lists of antimicrobials.6,8 While not intended to establish a standard of care, these guidelines complement antibiograms and contextualize antimicrobial choices. These guidelines in combination with antibiograms can inform clinical decision-making during the lag time between diagnosis of disease and receipt of an AST report from the diagnostic laboratory. Because these antibiograms were generated on the basis of results for samples submitted by a select group of hospitals, they should only be used by the practices that contributed to the present study. The antibiograms are provided to help explain the methodology and illustrate the benefits and challenges of creating antibiograms.

Guidelines from CLSI recommend including susceptibility results for all drugs tested when creating an antibiogram, rather than only the subset of drugs listed on the AST report, for which some results may be suppressed, and supplementary testing might be done only if certain resistance profiles are seen with the primary AST panel.12 Although this might be possible at a human hospital or veterinary teaching hospital with an internal clinical microbiology laboratory that has access to the full MIC testing data, this is unrealistic for PPs. Unlike an academic clinical microbiology laboratory, which would be able to manually retrieve results suppressed by the laboratory testing platform, PPs would only be able to analyze results for antimicrobial drugs listed on AST reports. Conversely, laboratories might list antimicrobial drugs against which a particular pathogen has intrinsic resistance or for which AST results are considered unlikely to be predictive of a clinical response. Therefore, veterinarians should familiarize themselves with standard lists of pathogens with intrinsic resistance.14,19

A major limitation identified in past studies18,23–25 is that the patient population for veterinary teaching hospitals typically consists of the most severely affected animals. Thus, results may not be generalizable to patient populations for first-opinion PPs. In the present study, we found that the characteristics of patients for which samples were submitted for culture and AST and the characteristics of patients that had samples with clinically relevant growth were generally similar between PPs and the APCP. However, our results did highlight the challenges of combining AST results from more than 1 laboratory, because the commercial and academic clinical microbiology laboratories used different testing platformsa,b and had unique suppression and supplemental testing algorithms, as inferred from the variations in antimicrobial drugs reported. Although both laboratories reported using CLSI breakpoints, it was not clear which version was being used or when each laboratory updated its breakpoints to meet the most recent guidelines published in 2018.14

Owing to differing testing and reporting mechanisms among laboratories, antibiograms should only be developed from results for samples analyzed by a single laboratory. In addition, veterinarians should check that the laboratory to which they are submitting samples follows standard guidelines for AST methods, including, ideally, broth dilution testing to determine MIC, and uses MIC breakpoints that comply with the latest available standards. Practitioners can also compare the antimicrobial drugs listed on AST reports they receive from their laboratory with those considered as standard to see how well they align.14,20

Following completion of the present study, we developed a potential workflow for a practice or practice group that wanted to create its own antibiogram on the basis of samples from a particular site or on the basis of isolates of a particular bacterial species or bacterial group (Figure 2). Results for samples for which no growth, growth of mixed flora only, growth of normal flora only, or growth only in thioglycolate broth was reported should be excluded, along with results for bacteria isolated from free-catch urine samples at concentrations < 10,000 CFUs/mL. In addition, results should be included only for the first isolate of a given species from any patient. These antibiograms could then be used in conjunction with rapid, inexpensive benchtop tests (eg, modified Wright- or Gram-staining of urine sediment or cytologic examination of pustule or tape specimens from skin lesions) to aid in empirical antimicrobial drug selection in a manner that supports antimicrobial stewardship principles.17,26–33

Figure 2—
Figure 2—

Flow diagram illustrating a method for a practice or practice group to create antibiograms on the basis of samples from a particular site or on the basis of isolates of a particular bacterial species or bacterial group.

Citation: Journal of the American Veterinary Medical Association 257, 9; 10.2460/javma.257.9.950

Antibiograms are not a replacement for but rather a complement to traditional culture and AST. Although antibiograms support empirical decision-making, veterinarians are encouraged to reassess their antimicrobial drug choice once culture and AST results are available, a concept called an antimicrobial time out.3,5 On the basis of this assessment, a decision may be made to discontinue 1 or more of the antimicrobials chosen empirically (ie, antimicrobial de-escalation).3–5,7,8 In addition to being location specific, antibiograms must remain current because patterns of resistance are expected to change over time. Annual renewal of antibiograms is recommended.

Acknowledgments

No third-party funding or support was received in connection with this study or the writing or publication of the manuscript. The authors declare that there were no conflicts of interest.

The authors thank Vee Ringer and Patti Andrews for generating lists of patients billed for aerobic bacterial cultures, Vee Ringer for granting access to patient AST reports, and Sandra Horton for generating tables with patient AST results and retrieving suppressed resistance data from the microbiology laboratory system.

ABBREVIATIONS

APCP

Academic primary care practice

AST

Antimicrobial susceptibility testing

CFU

Colony-forming unit

CLSI

Clinical and Laboratory Standards Institute

ISCAID

International Society for Companion Animal Infectious Diseases

MIC

Minimum inhibitory concentration

PP

Private practice

Footnotes

a.

Vitek 2, bioMériux, Durham, NC.

b.

Sensititre COMPGP1F/COMPGN1F, Thermo Scientific, Waltham, Mass.

c.

Excel, Microsoft Corp, Redmond, Wash.

d.

Easy Fisher exact test calculator, Social Science Statistics. Available at: www.socscistatistics.com/tests/fisher/default2.aspx. Accessed Jul 2, 2020.

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Appendix

Information required for constructing an antibiogram.

Patient information:
  Essential: Unique patient identification No.
  Preferred: Patient name, age (or date of birth), species, and sex and client last name.
Sample information:
  Essential: Unique laboratory accession No., sample type (eg, urine, fluid, or swab) or collection site (eg, skin), and date of collection.
  Preferred: Method of urine collection (eg, free catch, catheterization, or cystocentesis).
Isolate information:
  Essential: Genus and, if reported, species.
AST information:
  Essential: Susceptibility test method (eg, MIC), quantitative test measurement (eg, MIC), and interpretation (susceptible, intermediate, or resistant).
  Preferred: Specific testing system used (eg, broth microdilution or commercial system).

Adapted from CLSI guidelines12 for the analysis and presentation of cumulative AST data for human hospital antibiograms.

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