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. 2021 Feb 23;10(2):221.
doi: 10.3390/antibiotics10020221.

Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis

Ashenafi F Beyi  1 , Alan Hassall  2 , Gregory J Phillips  1 , Paul J Plummer  1   2   3
Affiliations

Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis

Ashenafi F Beyi et al. Antibiotics (Basel). .

Abstract

Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with ≥80% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.

Keywords: Hi-C ProxiMeta; antimicrobial resistance genes; digital dermatitis; resistomes; tetracycline resistance.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree of Spirochaetes, Bacteroidetes, Mycoplasma, and Bacteria from this study and reference organisms (which are labeled as “ref.”). In the construction of this dendrogram, we included the sequences of selected organisms identified in the current study and previous studies as well reference organisms, and PATRIC online tool (https://www.patricbrc.org/app/PhylogeneticTree (accessed on 22 February 2021)) was used.
Figure 2
Figure 2
Numbers of bacterial clusters with ≥80% complete genome coverage carrying tetracycline resistance genes.
See this image and copyright information in PMC

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