Analysis of the lung microbiota in dogs with Bordetella bronchiseptica infection and correlation with culture and quantitative polymerase chain reaction.

Infection with Bordetella bronchiseptica (Bb) can be confirmed using bacterial culture or quantitative polymerase chain reaction (qPCR). The lung microbiota (LM), which has been described in healthy experimental dogs, has not yet been studied in dogs with lower respiratory infection. In the present study we aimed to analyze the LM in dogs with Bb infection compared with healthy dogs, and to correlate the 16S rDNA amplicon sequencing results with culture and qPCR results.
Twenty dogs with a diagnosis of Bb infection obtained either by qPCR and/or culture and 4 healthy dogs were included. 16S rDNA sequences were obtained from naïve bronchoalveolar lavage fluid (BALF) after DNA extraction, PCR targeting the V1-V3 region of the 16S rDNA and sequencing.
Sequencing results showed the presence of Bb in all diseased dogs. About half of the dogs were co-infected, the majority with M. cynos. In diseased dogs, a shift in the β-diversity of the LM was observed (P=0.002); the richness and the α-diversity were significantly lower (P=0.012 and 0.006) and the bacterial load higher (P=0.004) compared with healthy dogs. Bb qPCR level and culture results were positively correlated with the relative abundance of Bb species after sequencing (r= 0.56, P=0.028 and r=0.70, P=0.002).
Bb induced a major dysbiosis of the LM, characterized by high bacterial load, low richness and diversity and increased abundance of Bb, in comparison with healthy dogs. Results of the LM analysis highly correlate with results obtained by qPCR and culture and show that results of LM can be reliable for identification of potentially causal bacterial microorganism involved in lung infectious diseases.