Genetic and phenotypic characteristics of Clostridium (Clostridioides) difficile from canine, bovine, and pediatric populations.

OBJECTIVES: Carriage of Clostridioides difficile by different species of animals has led to speculation that animals could represent a reservoir of this pathogen for human infections. The objective of this study was to compare C. difficile isolates from humans, dogs, and cattle from a restricted geographic area. METHODS: C. difficile isolates from 36 dogs and 15 dairy calves underwent whole genome sequencing, and phenotypic assays assessing growth and virulence were performed. Genomes of animal-derived isolates were compared to 29 genomes of isolates from a pediatric population as well as 44 reference genomes. RESULTS: Growth rates and relative cytotoxicity of isolates were significantly higher and lower, respectively, in bovine-derived isolates compared to pediatric- and canine-derived isolates. Analysis of core genes showed clustering by host species, though in a few cases, human strains co-clustered with canine or bovine strains, suggesting possible interspecies transmission. Geographic differences (e.g., farm, litter) were small compared to differences between species. In an analysis of accessory genes, the total number of genes in each genome varied between host species, with 6.7% of functional orthologs differentially present/absent between host species and bovine-derived strains having the lowest number of genes. Canine-derived isolates were most likely to be non-toxigenic and more likely to carry phages. A targeted study of episomes identified in local pediatric strains showed sharing of a methicillin-resistance plasmid with dogs, and historic sharing of a wide range of episomes across hosts. Bovine-derived isolates harbored the widest variety of antibiotic-resistance genes, followed by canine CONCLUSIONS: While C. difficile isolates mostly clustered by host species, occasional co-clustering of canine and pediatric-derived isolates suggests the possibility of interspecies transmission. The presence of a pool of resistance genes in animal-derived isolates with the potential to appear in humans given sufficient pressure from antibiotic use warrants concern.

Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients.

Few studies have examined the lung virome in health and disease. Outcomes of lung transplantation are known to be influenced by several recognized respiratory viruses, but global understanding of the virome of the transplanted lung is incomplete. To define the DNA virome within the respiratory tract following lung transplantation we carried out metagenomic analysis of allograft bronchoalveolar lavage (BAL), and compared with healthy and HIV+ subjects. Viral concentrates were purified from BAL and analyzed by shotgun DNA sequencing. All of the BAL samples contained reads mapping to anelloviruses, with high proportions in lung transplant samples. Anellovirus populations in transplant recipients were complex, with multiple concurrent variants. Quantitative polymerase chain reaction quantification revealed that anellovirus sequences were 56-fold more abundant in BAL from lung transplant recipients compared with healthy controls or HIV+ subjects (p < 0.0001). Anellovirus sequences were also more abundant in upper respiratory tract specimens from lung transplant recipients than controls (p = 0.006). Comparison to metagenomic data on bacterial populations showed that high anellovirus loads correlated with dysbiotic bacterial communities in allograft BAL (p = 0.008). Thus the respiratory tracts of lung transplant recipients contain high levels and complex populations of anelloviruses, warranting studies of anellovirus lung infection and transplant outcome.

Temporal dynamics in the ruminal microbiome of dairy cows during the transition period.

The transition period in dairy cows refers to the period from 3 wk before calving to 3 wk post-calving and is a critical time for influencing milk production and cow health. We hypothesize that the ruminal microbiome shifts as dairy cows transition from a non-lactation period into lactation due to changes in dietary regimen. The purpose of this study was to identify differences in the ruminal microbiome of primiparous and multiparous (study group) cows during the transition period. Five primiparous and 5 multiparous cows were randomly selected from a herd, and ruminal contents were sampled, via stomach tube, 4 times (study day) at 3 wk before calving date (S1), 1 to 3 d post-calving (S2), and 4 (S3) and 8 wk (S4) into lactation and were evaluated for bacterial diversity using 16S pyrotags. Both groups received the same pre-fresh diet (14.6% CP, 44.0% NDF, 21.9% starch) and 3 different lactation diets (L1, L2, and L3) varying in forage base but not amount and formulated to have similar nutrient specifications (16.8% to 17.7% CP; 32.5% to 33.6% NDF; 26.2% to 29.1% starch) post-calving. Forty bacterial communities were analyzed on the basis of annotations of 100,000 reads, resulting in 15,861 operational taxonomic units grouped into 17 bacterial phyla. The UniFrac distance metric revealed that both study group and study day had an effect on the community compositions (P < 0.05; permutational multivariate ANOVA test). The most abundant phyla observed were Bacteroidetes and Firmicutes across all the communities. As the cows transitioned into lactation, the ratio of Bacteroidetes to Firmicutes increased from 6:1 to 12:1 (P < 0.05; Mann-Whitney U test), and this ratio was greater in primiparous cows than in multiparous cows (P < 0.05). This report is the first to explore the effect of parity on dynamics in the ruminal microbiome of cows during the transition period.