External Ear Canal Evaluation in Dogs with Chronic Suppurative Otitis Externa: Comparison of Direct Cytology, Bacterial Culture and 16S Amplicon Profiling

SIMPLE SUMMARY: Discrepancy between the results of cytology and bacterial culture methods is sometimes observed in canine otitis externa. The objective of this study was to compare different techniques: direct cytology, aerobic bacterial culture and 16S amplicon profiling. Samples from twenty ears with chronic suppurative otitis externa were analysed. Good correlation between cytology and bacterial culture was observed in 60% of samples. Good correlation between bacterial culture and 16S amplicon profiling was observed in only 10% of samples when the overall 16S amplicon profiling results were used. Nevertheless, the correlation improved to 70% when bacterial species with a relative abundance >10% (considered as insignificant) were taken into account. Of the total bacterial species revealed by 16S amplicon profiling with relative abundance >10%, 38.7% of bacterial species were not revealed by bacterial culture; most of the time, the offending species was a Corynebacterium. This study showed that a careful interpretation of the result of the bacterial culture should be performed, and always with the support of cytology. To assess the overall bacterial population in suppurative otitis, the 16S amplicon profiling method seems to be a more accurate method but does not provide information on bacterial susceptibility. ABSTRACT: A discrepancy between cytology and bacterial culture methods is sometimes observed in canine otitis externa. The objective of this study was to compare results from cytology, bacterial culture and 16S amplicon profiling. Twenty samples from 16 dogs with chronic suppurative otitis externa were collected. A direct cytological evaluation was carried out during the consultations. Aerobic bacterial culture and susceptibility were performed by an external laboratory used in routine practice. For 16S amplicon profiling, DNA was extracted and the hypervariable segment V1–V3 of the 16S rDNA was amplified and then sequenced with a MiSeq Illumina sequence carried out by the Mothur software using the SILVA database. A good correlation between cytology and bacterial culture was observed in 60% of the samples. Some bacterial species revealed by bacterial culture were present with low relative abundance (<10%) in 16S amplicon profiling. Some bacterial species revealed by the 16S amplicon profiling analysis were not identified with culture; most of the time, the offending species was a Corynebacterium. To conclude, a careful interpretation of the results of bacterial culture should be made and always be in agreement with the cytology. The 16S amplicon profiling method appears to be a more sensitive method for detecting strains present in suppurative otitis but does not provide information on bacterial susceptibility.