Respiratory Dysbiosis in Canine Bacterial Pneumonia: Standard Culture vs. Microbiome Sequencing

Abstract

It is unknown how the respiratory microbiome influences and is influenced by bacterial pneumonia in dogs, as culture of lung samples and not microbial sequencing guides clinical practice. While accurate identification of pathogens are essential for treatment, not all bacteria are cultivable and the impact of respiratory dysbiosis on development of pneumonia is unclear. The study purposes were to (1) characterize the lung microbiome in canine bacterial pneumonia and compare deviations in dominant microbial populations with historical healthy controls, (2) compare bacteria identified by culture vs. 16S rDNA sequencing from bronchoalveolar lavage fluid (BALF) culture-, and (3) evaluate similarities in lung and oropharyngeal (OP) microbial communities in community-acquired and secondary bacterial pneumonia. Twenty BALF samples from 15 client-owned dogs diagnosed with bacterial pneumonia were enrolled. From a subset of dogs, OP swabs were collected. Extracted DNA underwent PCR of the 16S rRNA gene. Relative abundance of operational taxonomic units (OTUs) were determined. The relative abundance of bacterial community members found in health was decreased in dogs with pneumonia. Taxa identified via culture were not always the dominant phylotype identified with sequencing. Dogs with community-acquired pneumonia were more likely to have overgrowth of a single organism suggesting loss of dominant species associated with health. Dogs with secondary bacterial pneumonia had a greater regional continuity between the upper and lower airways. Collectively, these data suggest that dysbiosis occurs in canine bacterial pneumonia, and culture-independent techniques may provide greater depth of understanding of the changes in bacterial community composition that occur in disease.

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

“…Other bacteria with a relative abundance > 5% that have been associated with pneumonia such as Stenotrophomonas sp., Ureaplasma sp., Escherichia-Shigella sp. in dogs [5,30,[40][41][42], or Elizabethkingia meningoseptica in man [43] were found in that study. Although it is unclear if they are just colonizing or co-infecting bacteria, and if they could potentially play a role in CIRD-C.…”

“…Indeed, large dataset requires more severe corrections for multiple tests [39]. In dogs affected with B. bronchiseptica infection, in comparison with heathy dogs, the LM was composed in majority by only one or two bacteria, a finding that has also been reported in dogs with CAP [30]. In pneumonia in man, the dominant pathogenic strain also usually represents the majority of the detected sequences (74% or more) [24]; a low alphadiversity and low richness reflecting the high predominance of one or two bacteria are also described together with an increased bacterial load [26].…”

“…Studies in acute pneumonia indicate that the 16S rDNA sequencing improves the microbiological yield and could help to guide antimicrobial therapy [20,27]. In dogs, the lung microbiota (LM) has only been studied in bacterial secondary or community-acquired pneumonia (CAP) and only few data are available in experimental healthy beagles [28][29][30] and healthy dogs from other breeds [31]. In dogs with pneumonia, a dysbiosis of the LM was observed with the loss of bacteria found in health and the domination, mostly in CAP, of one or two bacteria [30].…”

“…In dogs, the lung microbiota (LM) has only been studied in bacterial secondary or community-acquired pneumonia (CAP) and only few data are available in experimental healthy beagles [28][29][30] and healthy dogs from other breeds [31]. In dogs with pneumonia, a dysbiosis of the LM was observed with the loss of bacteria found in health and the domination, mostly in CAP, of one or two bacteria [30]. Moreover a good agreement was found between the results of 16S rDNA amplicon sequencing and culture, although some discrepancies concerning the number of unique taxa identified and presence or absence of predominating taxa were noticed [30].…”

“…In dogs with pneumonia, a dysbiosis of the LM was observed with the loss of bacteria found in health and the domination, mostly in CAP, of one or two bacteria [30]. Moreover a good agreement was found between the results of 16S rDNA amplicon sequencing and culture, although some discrepancies concerning the number of unique taxa identified and presence or absence of predominating taxa were noticed [30]. Results suggest that the 16S rDNA amplicon sequencing could be useful for causal bacteria detection in parallel with culture, mostly if culture is negative [30].…”