Towards harmonized laboratory methodologies in veterinary clinical bacteriology: outcomes of a European survey

Abstract

Introduction: Veterinary clinical microbiology laboratories play a key role in antimicrobial stewardship, surveillance of antimicrobial resistance and prevention of healthcare associated-infections. However, there is a shortage of international harmonized guidelines covering all steps of veterinary bacterial culture from sample receipt to reporting.

Methods: In order to gain insights, the European Network for Optimization of Veterinary Antimicrobial Treatment (ENOVAT) designed an online survey focused on the practices and interpretive criteria used for bacterial culture and identification (C&ID), and antimicrobial susceptibility testing (AST) of animal bacterial pathogens.

Results: A total of 241 microbiology laboratories in 34 European countries completed the survey, representing a mixture of academic (37.6%), governmental (27.4%), and private (26.5%) laboratories. The C&ID turnaround varied from 1 to 2 days (77.8%) to 3-5 days (20%), and 6- 8 days (1.6%), with similar timeframes for AST. Individual biochemical tests and analytical profile index (API) biochemical test kits or similar were the most frequent tools used for bacterial identification (77% and 56.2%, respectively), followed by PCR (46.6%) and MALDI-TOF MS (43.3%). For AST, Kirby-Bauer disk diffusion (DD) and minimum inhibitory concentration (MIC) determination were conducted by 43.8% and 32.6% of laboratories, respectively, with a combination of EUCAST and CLSI clinical breakpoints (CBPs) preferred for interpretation of the DD (41.2%) and MIC (47.6%) results. In the absence of specific CBPs, laboratories used human CBPs (53.3%) or veterinary CBPs representing another body site, organism or animal species (51.5%). Importantly, most laboratories (47.9%) only report the qualitative interpretation of the result (S, R, and I). As regards testing for AMR mechanisms, 48.5% and 46.7% of laboratories routinely screened isolates for methicillin resistance and ESBL production, respectively. Notably, selective reporting of AST results (i.e. excluding highest priority critically important antimicrobials from AST reports) was adopted by 39.5% of laboratories despite a similar proportion not taking any approach (37.6%) to guide clinicians towards narrower-spectrum or first-line antibiotics.

Discussion: In conclusion, we identified a broad variety of methodologies and interpretative criteria used for C&ID and AST in European veterinary microbiological diagnostic laboratories. The observed gaps in veterinary microbiology practices emphasize a need to improve and harmonize professional training, innovation, bacterial culture methods and interpretation, AMR surveillance and reporting strategies.

Keywords: ENOVAT; antimicrobial susceptibility testing; bacterial culture; bacterial identification; harmonization; methodologies; veterinary clinical bacteriology.

FIGURE 1

Geographic distribution of survey responders across Europe.

FIGURE 2

Number of clinical specimens processed for bacteriology by the laboratories based on the main sector in which they are functioning.

FIGURE 3

Figures for questions Q20–Q25. Responses regarding the methodology employed by the participating laboratories for bacterial culture and antimicrobial susceptibility testing. Percentages are based on the number of responses to individual questions. MA, multiple answer question; SA, single answer question. Q20–Identification to species level (SA); Q21–Methods for bacterial identification (MA); Q22–AST method provided (MA); Q23–MIC method provided (MA); Q24-1–Main clinical breakpoints (CBP) used for disc diffusion (SA), Q24-2–Main clinical breakpoints used for MIC (SA); Q25–Approach when no species–specific CBPs (MA).

FIGURE 4

Responses to question Q27 on reasons for phenotypical screening of various resistant bacteria. For each type of resistant bacteria listed, multiple answers were possible. Valid answers were considered if participants interacted with at least one of the questions in a row of the table (see Supplementary Table 3). MA, multiple answers.