The present study highlights challenges in the veterinary microbiology diagnostic laboratory in the identification of bacteria responsible for infections in veterinary settings, particularly when evidence-based data is lacking. A 1.8-year-old neutered male domestic cat (FIV/FeLV negative) was presented to a veterinary practice in April 2016 with a history of left unilateral mild conjunctivitis that was empirically treated with fusidic acid and chloramphenicol. In January 2017, the same animal was presented with chronic left unilateral conjunctivitis and an eye swab was submitted for microbiological culture and susceptibility testing. Significant growth was not detected in two samples tested. Finally, in February 2017 another eye swab produced a slow growing pure culture identified by VITEK 2 as Neisseria cinerea (94 % confidence). Given the morphology and multidrug resistance profile of the isolate a 16S rRNA PCR was performed for definitive identification. The nucleotide sequence of the PCR amplicon was 99 % homologous to Acinetobacter equi sp. nov. strain 114. Veterinary microbiology diagnostic laboratories play an important role worldwide, not only in preserving animal health and welfare but also in controlling the spread of zoonotic pathogens. The lack of evidence-based information on the ocular microbiome of healthy cats and the complexity of bacterial ecosystems renders the interpretation of results difficult. A further problem for both the laboratory and the clinician is the lack of interpretive criteria for antibiotic susceptibility test results for some types of infections in animals (including those caused by Acinetobacter ) and the complete unavailability of criteria for topical antibiotic preparations.